{"lab": {"title": "Mitchell Guttman, CALTECH", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "correspondence": [{"contact_email": "bWd1dHRtYW5AY2FsdGVjaC5lZHU=", "@id": "/users/ac3920c8-caa6-444b-be8a-48b52a1dcb3e/", "display_title": "Mitchell Guttman"}], "display_title": "Mitchell Guttman, CALTECH", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "award": {"display_title": "DECIPHERING THE FUNCTION AND MECHANISMS OF LNCRNA-MEDIATED ORGANIZATION OF NUCLEAR COMPARTMENTS", "@type": ["Award", "Item"], "name": "1U01DA040612-01", "uuid": "4de1cf81-1ea0-4a19-bc7a-dd3343b34438", "description": "NBC: The nucleus of each cell is a complex arrangement of DNA, RNA, and protein that is dynamically organized into various nuclear bodies and compartments that are often arranged around shared functional and regulatory roles. Yet, while many of these nuclear compartments were first identified several decades ago a major challenge with characterizing these compartments is that there are currently no biochemical methods for isolating individual nuclear compartments. Importantly, many nuclear bodies are marked and maintained by nuclear retained long non-coding RNAs (lncRNAs). Here we aim to develop several novel technologies to purify the molecular constituents of nuclear domains and their necessity and sufficiency in forming these compartments. Together these technologies will allow us to systematically address the following questions: Aim 1: What are the optimal biochemical conditions in which to specifically and accurately purify specific nuclear bodies and compartments in order to identify their DNA, RNA and protein components? A critical aspect of biochemical purifications is the fine balance between cross-linking conditions that identify direct molecular interactions while not over-crosslinking that could result in indirect interactions. Usin known nuclear compartments such as the nucleolus, nuclear speckles, and paraspeckles we will optimize RAP for isolating DNA-RNA, RNA-RNA, RNA-protein interactions. We aim to identify universally applicable purification conditions to identify molecular interactions within nuclear and other subcellular structures. Aim 2: What are the DNA, RNA and protein factors involved in nuclear compartments? Although most known nuclear bodies are characterized by lncRNAs the other RNA, DNA and protein factors remain less well defined. Here we will develop technologies to catalog the molecular factors that comprise various nuclear bodies. We will further validate these components through colocalization of these components within a nuclear domain using visualization approaches (e.g. RNA-DNA Co-FISH). Overall we aim to apply new technologies to systematic and comprehensive catalog of RNA, DNA and Proteins in nuclear bodies. Aim 3: Are lncRNAs and proteins necessary and/or sufficient for nuclear compartmentalization? Here we will develop a novel technology platform, termed CRISPR-Display, which allows long RNA cargos to be appended and delivered by CRISPR-Cas9 systems to a desired site in the genome. We will develop this technology to test if lncRNA molecules are sufficient to drive nuclear organization. We will also use CRISPR-Display to multiplex several RNA aptamers that can be used to recruit proteins (with reciprocal protein epitopes that bind RNA aptamers) and test if they are sufficient to form nuclear compartments. In parallel we will perform loss-of- function approaches to identify protein and or RNA components are required for establishing nuclear domains. Collectively our proposal aims to develop powerful and multifaceted technologies to catalog the molecular components of subnuclear structures, validate these interactions and test their biological importance.", "center_title": "NBC - Guttman", "@id": "/awards/1U01DA040612-01/", "status": "current", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIEQJ8QSC/", "uuid": "39f2bc1d-ce8d-4775-a3d4-47d268e2ed2f", "upload_key": "39f2bc1d-ce8d-4775-a3d4-47d268e2ed2f/4DNFIEQJ8QSC.fastq.gz", "file_type": "reads", "file_size": 2806710698, "accession": "4DNFIEQJ8QSC", "display_title": "4DNFIEQJ8QSC.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIEQJ8QSC/@@download/4DNFIEQJ8QSC.fastq.gz", "quality_metric": {"uuid": "d784fa79-2efe-4498-b480-7b949091a49d", "Total Sequences": 43608728, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEQJ8QSC/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/d784fa79-2efe-4498-b480-7b949091a49d/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIYYYJ98O", "file_type": "reads", "display_title": "4DNFIYYYJ98O.fastq.gz", "paired_end": "2", "uuid": "25b77bbe-7c13-42a4-8f0b-952b768c424b", "@id": "/files-fastq/4DNFIYYYJ98O/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIYYYJ98O/", "uuid": "25b77bbe-7c13-42a4-8f0b-952b768c424b", "upload_key": "25b77bbe-7c13-42a4-8f0b-952b768c424b/4DNFIYYYJ98O.fastq.gz", "file_type": "reads", "file_size": 3564242054, "accession": "4DNFIYYYJ98O", "display_title": "4DNFIYYYJ98O.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIYYYJ98O/@@download/4DNFIYYYJ98O.fastq.gz", "quality_metric": {"uuid": "d089167b-b4f1-4925-8ebc-ff6d67c64d92", "Total Sequences": 43608728, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYYYJ98O/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/d089167b-b4f1-4925-8ebc-ff6d67c64d92/", "Sequence length": "78-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIEQJ8QSC", "file_type": "reads", "display_title": "4DNFIEQJ8QSC.fastq.gz", "paired_end": "1", "uuid": "39f2bc1d-ce8d-4775-a3d4-47d268e2ed2f", "@id": "/files-fastq/4DNFIEQJ8QSC/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFISIEMG4R/", "uuid": "dd5892af-3fa1-4abb-98bb-f631ebd3556a", "upload_key": "dd5892af-3fa1-4abb-98bb-f631ebd3556a/4DNFISIEMG4R.fastq.gz", "file_type": "reads", "file_size": 2042425052, "accession": "4DNFISIEMG4R", "display_title": "4DNFISIEMG4R.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFISIEMG4R/@@download/4DNFISIEMG4R.fastq.gz", "quality_metric": {"uuid": "3c029be8-158e-4402-8d8d-af1349d30431", "Total Sequences": 31514416, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISIEMG4R/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/3c029be8-158e-4402-8d8d-af1349d30431/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFISFG1FAE", "file_type": "reads", "display_title": "4DNFISFG1FAE.fastq.gz", "paired_end": "2", "uuid": "2ec0293e-aa91-4853-a9ec-06c58bc2ca28", "@id": "/files-fastq/4DNFISFG1FAE/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFISFG1FAE/", "uuid": "2ec0293e-aa91-4853-a9ec-06c58bc2ca28", "upload_key": "2ec0293e-aa91-4853-a9ec-06c58bc2ca28/4DNFISFG1FAE.fastq.gz", "file_type": "reads", "file_size": 2575773369, "accession": "4DNFISFG1FAE", "display_title": "4DNFISFG1FAE.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFISFG1FAE/@@download/4DNFISFG1FAE.fastq.gz", "quality_metric": {"uuid": "7595ebe1-f564-4e96-ae0e-55bc2283974b", "Total Sequences": 31514416, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISFG1FAE/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/7595ebe1-f564-4e96-ae0e-55bc2283974b/", "Sequence length": "77-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFISIEMG4R", "file_type": "reads", "display_title": "4DNFISIEMG4R.fastq.gz", "paired_end": "1", "uuid": "dd5892af-3fa1-4abb-98bb-f631ebd3556a", "@id": "/files-fastq/4DNFISIEMG4R/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFI71NWZ9Z/", "uuid": "a6ab09a5-20a8-4ef6-a42e-b2b775b74c2e", "upload_key": "a6ab09a5-20a8-4ef6-a42e-b2b775b74c2e/4DNFI71NWZ9Z.fastq.gz", "file_type": "reads", "file_size": 2721623792, "accession": "4DNFI71NWZ9Z", "display_title": "4DNFI71NWZ9Z.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFI71NWZ9Z/@@download/4DNFI71NWZ9Z.fastq.gz", "quality_metric": {"uuid": "2a71c9c4-4114-4487-b806-12561350fc4e", "Total Sequences": 42100128, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI71NWZ9Z/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/2a71c9c4-4114-4487-b806-12561350fc4e/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIV6DU54R", "file_type": "reads", "display_title": "4DNFIV6DU54R.fastq.gz", "paired_end": "2", "uuid": "18da9569-7d54-4030-bfa3-5ba6f88d9a28", "@id": "/files-fastq/4DNFIV6DU54R/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIV6DU54R/", "uuid": "18da9569-7d54-4030-bfa3-5ba6f88d9a28", "upload_key": "18da9569-7d54-4030-bfa3-5ba6f88d9a28/4DNFIV6DU54R.fastq.gz", "file_type": "reads", "file_size": 3438443399, "accession": "4DNFIV6DU54R", "display_title": "4DNFIV6DU54R.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIV6DU54R/@@download/4DNFIV6DU54R.fastq.gz", "quality_metric": {"uuid": "259c696f-11b5-42e8-ba2a-7793774beb76", "Total Sequences": 42100128, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV6DU54R/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/259c696f-11b5-42e8-ba2a-7793774beb76/", "Sequence length": "77-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI71NWZ9Z", "file_type": "reads", "display_title": "4DNFI71NWZ9Z.fastq.gz", "paired_end": "1", "uuid": "a6ab09a5-20a8-4ef6-a42e-b2b775b74c2e", "@id": "/files-fastq/4DNFI71NWZ9Z/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFI5Q6PZHV/", "uuid": "1df1250b-fb1f-4b5d-9783-b7379a0a4e46", "upload_key": "1df1250b-fb1f-4b5d-9783-b7379a0a4e46/4DNFI5Q6PZHV.fastq.gz", "file_type": "reads", "file_size": 2234693494, "accession": "4DNFI5Q6PZHV", "display_title": "4DNFI5Q6PZHV.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFI5Q6PZHV/@@download/4DNFI5Q6PZHV.fastq.gz", "quality_metric": {"uuid": "1956632e-a629-4291-aba1-646d9f2f0330", "Total Sequences": 34270733, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5Q6PZHV/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/1956632e-a629-4291-aba1-646d9f2f0330/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIZDPJWRN", "file_type": "reads", "display_title": "4DNFIZDPJWRN.fastq.gz", "paired_end": "2", "uuid": "79c4edfa-eb4f-49a4-be44-b390a2271395", "@id": "/files-fastq/4DNFIZDPJWRN/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIZDPJWRN/", "uuid": "79c4edfa-eb4f-49a4-be44-b390a2271395", "upload_key": "79c4edfa-eb4f-49a4-be44-b390a2271395/4DNFIZDPJWRN.fastq.gz", "file_type": "reads", "file_size": 2818402633, "accession": "4DNFIZDPJWRN", "display_title": "4DNFIZDPJWRN.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIZDPJWRN/@@download/4DNFIZDPJWRN.fastq.gz", "quality_metric": {"uuid": "9485c5a8-3dea-4421-8be5-20498ee062bb", "Total Sequences": 34270733, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZDPJWRN/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/9485c5a8-3dea-4421-8be5-20498ee062bb/", "Sequence length": "78-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI5Q6PZHV", "file_type": "reads", "display_title": "4DNFI5Q6PZHV.fastq.gz", "paired_end": "1", "uuid": "1df1250b-fb1f-4b5d-9783-b7379a0a4e46", "@id": "/files-fastq/4DNFI5Q6PZHV/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFID7SBWRR/", "uuid": "a86ff718-95a3-40c3-abe7-00f2336f49aa", "upload_key": "a86ff718-95a3-40c3-abe7-00f2336f49aa/4DNFID7SBWRR.fastq.gz", "file_type": "reads", "file_size": 3095454942, "accession": "4DNFID7SBWRR", "display_title": "4DNFID7SBWRR.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFID7SBWRR/@@download/4DNFID7SBWRR.fastq.gz", "quality_metric": {"uuid": "090b697a-4c19-4630-b4b7-c2c84e260f36", "Total Sequences": 48059508, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID7SBWRR/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/090b697a-4c19-4630-b4b7-c2c84e260f36/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFINJB6JTN", "file_type": "reads", "display_title": "4DNFINJB6JTN.fastq.gz", "paired_end": "2", "uuid": "e0f035df-a9b4-4794-ac62-dc5ccad0a357", "@id": "/files-fastq/4DNFINJB6JTN/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFINJB6JTN/", "uuid": "e0f035df-a9b4-4794-ac62-dc5ccad0a357", "upload_key": "e0f035df-a9b4-4794-ac62-dc5ccad0a357/4DNFINJB6JTN.fastq.gz", "file_type": "reads", "file_size": 3943454603, "accession": "4DNFINJB6JTN", "display_title": "4DNFINJB6JTN.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFINJB6JTN/@@download/4DNFINJB6JTN.fastq.gz", "quality_metric": {"uuid": "109371ec-7538-4b09-871c-7e3c00d0832c", "Total Sequences": 48059508, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINJB6JTN/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/109371ec-7538-4b09-871c-7e3c00d0832c/", "Sequence length": "78-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFID7SBWRR", "file_type": "reads", "display_title": "4DNFID7SBWRR.fastq.gz", "paired_end": "1", "uuid": "a86ff718-95a3-40c3-abe7-00f2336f49aa", "@id": "/files-fastq/4DNFID7SBWRR/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFI3HREHZ2/", "uuid": "098cdd27-1905-4047-b6d9-2aa257c1ff98", "upload_key": "098cdd27-1905-4047-b6d9-2aa257c1ff98/4DNFI3HREHZ2.fastq.gz", "file_type": "reads", "file_size": 3221620800, "accession": "4DNFI3HREHZ2", "display_title": "4DNFI3HREHZ2.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFI3HREHZ2/@@download/4DNFI3HREHZ2.fastq.gz", "quality_metric": {"uuid": "3316e049-bcfb-443c-bb8f-d4b3e9f96110", "Total Sequences": 50322330, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3HREHZ2/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/3316e049-bcfb-443c-bb8f-d4b3e9f96110/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIMXVP9O1", "file_type": "reads", "display_title": "4DNFIMXVP9O1.fastq.gz", "paired_end": "2", "uuid": "27ea05ab-cf6b-42a5-b29b-4724bc194cc1", "@id": "/files-fastq/4DNFIMXVP9O1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIMXVP9O1/", "uuid": "27ea05ab-cf6b-42a5-b29b-4724bc194cc1", "upload_key": "27ea05ab-cf6b-42a5-b29b-4724bc194cc1/4DNFIMXVP9O1.fastq.gz", "file_type": "reads", "file_size": 4037029482, "accession": "4DNFIMXVP9O1", "display_title": "4DNFIMXVP9O1.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIMXVP9O1/@@download/4DNFIMXVP9O1.fastq.gz", "quality_metric": {"uuid": "be4bd463-f340-460f-abcc-53b9d90d0edf", "Total Sequences": 50322330, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMXVP9O1/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/be4bd463-f340-460f-abcc-53b9d90d0edf/", "Sequence length": "77-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI3HREHZ2", "file_type": "reads", "display_title": "4DNFI3HREHZ2.fastq.gz", "paired_end": "1", "uuid": "098cdd27-1905-4047-b6d9-2aa257c1ff98", "@id": "/files-fastq/4DNFI3HREHZ2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIGIHC7MP/", "uuid": "ac1b1733-3add-4949-9a38-c8a0953283ec", "upload_key": "ac1b1733-3add-4949-9a38-c8a0953283ec/4DNFIGIHC7MP.fastq.gz", "file_type": "reads", "file_size": 3019251176, "accession": "4DNFIGIHC7MP", "display_title": "4DNFIGIHC7MP.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIGIHC7MP/@@download/4DNFIGIHC7MP.fastq.gz", "quality_metric": {"uuid": "d098b46d-230f-4657-97a9-34be03ddeef9", "Total Sequences": 46653014, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGIHC7MP/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/d098b46d-230f-4657-97a9-34be03ddeef9/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFICKXP3IO", "file_type": "reads", "display_title": "4DNFICKXP3IO.fastq.gz", "paired_end": "2", "uuid": "e2fd22a3-226d-4fc2-93b8-09ca85fb9b00", "@id": "/files-fastq/4DNFICKXP3IO/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFICKXP3IO/", "uuid": "e2fd22a3-226d-4fc2-93b8-09ca85fb9b00", "upload_key": "e2fd22a3-226d-4fc2-93b8-09ca85fb9b00/4DNFICKXP3IO.fastq.gz", "file_type": "reads", "file_size": 3752673582, "accession": "4DNFICKXP3IO", "display_title": "4DNFICKXP3IO.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFICKXP3IO/@@download/4DNFICKXP3IO.fastq.gz", "quality_metric": {"uuid": "a7326ac7-b49f-4d79-a5fa-99a5169c587a", "Total Sequences": 46653014, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICKXP3IO/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/a7326ac7-b49f-4d79-a5fa-99a5169c587a/", "Sequence length": "78-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIGIHC7MP", "file_type": "reads", "display_title": "4DNFIGIHC7MP.fastq.gz", "paired_end": "1", "uuid": "ac1b1733-3add-4949-9a38-c8a0953283ec", "@id": "/files-fastq/4DNFIGIHC7MP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFICZMS3PW/", "uuid": "9e7f7e55-e918-409b-a260-ecbfc19328f6", "upload_key": "9e7f7e55-e918-409b-a260-ecbfc19328f6/4DNFICZMS3PW.fastq.gz", "file_type": "reads", "file_size": 1566323767, "accession": "4DNFICZMS3PW", "display_title": "4DNFICZMS3PW.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFICZMS3PW/@@download/4DNFICZMS3PW.fastq.gz", "quality_metric": {"uuid": "2eebe48b-a3d5-423b-8b09-54a71f3324d8", "Total Sequences": 22770033, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICZMS3PW/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/2eebe48b-a3d5-423b-8b09-54a71f3324d8/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFINUTTPTE", "file_type": "reads", "display_title": "4DNFINUTTPTE.fastq.gz", "paired_end": "2", "uuid": "ead13a06-b024-4aa2-bec2-ea4e899d7aca", "@id": "/files-fastq/4DNFINUTTPTE/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFINUTTPTE/", "uuid": "ead13a06-b024-4aa2-bec2-ea4e899d7aca", "upload_key": "ead13a06-b024-4aa2-bec2-ea4e899d7aca/4DNFINUTTPTE.fastq.gz", "file_type": "reads", "file_size": 1851414153, "accession": "4DNFINUTTPTE", "display_title": "4DNFINUTTPTE.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFINUTTPTE/@@download/4DNFINUTTPTE.fastq.gz", "quality_metric": {"uuid": "72861ea5-cad0-465b-91b2-27355949a592", "Total Sequences": 22770033, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINUTTPTE/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/72861ea5-cad0-465b-91b2-27355949a592/", "Sequence length": "78-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFICZMS3PW", "file_type": "reads", "display_title": "4DNFICZMS3PW.fastq.gz", "paired_end": "1", "uuid": "9e7f7e55-e918-409b-a260-ecbfc19328f6", "@id": "/files-fastq/4DNFICZMS3PW/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIX2RCABF/", "uuid": "f37c6cd9-2b81-4805-b6e1-dba46c6406d8", "upload_key": "f37c6cd9-2b81-4805-b6e1-dba46c6406d8/4DNFIX2RCABF.fastq.gz", "file_type": "reads", "file_size": 1097450844, "accession": "4DNFIX2RCABF", "display_title": "4DNFIX2RCABF.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIX2RCABF/@@download/4DNFIX2RCABF.fastq.gz", "quality_metric": {"uuid": "f01c66fd-8d47-4192-9d68-862b8e606ebc", "Total Sequences": 16050280, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX2RCABF/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/f01c66fd-8d47-4192-9d68-862b8e606ebc/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI6Z69P2Q", "file_type": "reads", "display_title": "4DNFI6Z69P2Q.fastq.gz", "paired_end": "2", "uuid": "77304811-ee8a-496c-8bf5-13c3ecc95526", "@id": "/files-fastq/4DNFI6Z69P2Q/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFI6Z69P2Q/", "uuid": "77304811-ee8a-496c-8bf5-13c3ecc95526", "upload_key": "77304811-ee8a-496c-8bf5-13c3ecc95526/4DNFI6Z69P2Q.fastq.gz", "file_type": "reads", "file_size": 1300629557, "accession": "4DNFI6Z69P2Q", "display_title": "4DNFI6Z69P2Q.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFI6Z69P2Q/@@download/4DNFI6Z69P2Q.fastq.gz", "quality_metric": {"uuid": "df777008-8ede-4301-a9ee-ea905a8908e4", "Total Sequences": 16050280, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6Z69P2Q/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/df777008-8ede-4301-a9ee-ea905a8908e4/", "Sequence length": "77-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIX2RCABF", "file_type": "reads", "display_title": "4DNFIX2RCABF.fastq.gz", "paired_end": "1", "uuid": "f37c6cd9-2b81-4805-b6e1-dba46c6406d8", "@id": "/files-fastq/4DNFIX2RCABF/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIJ517P4F/", "uuid": "810c60d1-fdcd-430f-b8b3-e355ae47d049", "upload_key": "810c60d1-fdcd-430f-b8b3-e355ae47d049/4DNFIJ517P4F.fastq.gz", "file_type": "reads", "file_size": 1558895463, "accession": "4DNFIJ517P4F", "display_title": "4DNFIJ517P4F.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIJ517P4F/@@download/4DNFIJ517P4F.fastq.gz", "quality_metric": {"uuid": "67906deb-5eb4-4898-a59d-bfbd4f83c5f7", "Total Sequences": 22765298, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJ517P4F/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/67906deb-5eb4-4898-a59d-bfbd4f83c5f7/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIZQV5G32", "file_type": "reads", "display_title": "4DNFIZQV5G32.fastq.gz", "paired_end": "2", "uuid": "c10877d3-afc9-4feb-aaae-d67d850db9ea", "@id": "/files-fastq/4DNFIZQV5G32/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIZQV5G32/", "uuid": "c10877d3-afc9-4feb-aaae-d67d850db9ea", "upload_key": "c10877d3-afc9-4feb-aaae-d67d850db9ea/4DNFIZQV5G32.fastq.gz", "file_type": "reads", "file_size": 1836437724, "accession": "4DNFIZQV5G32", "display_title": "4DNFIZQV5G32.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIZQV5G32/@@download/4DNFIZQV5G32.fastq.gz", "quality_metric": {"uuid": "72b4a5d7-97ae-4fef-a5de-328d504e21b5", "Total Sequences": 22765298, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZQV5G32/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/72b4a5d7-97ae-4fef-a5de-328d504e21b5/", "Sequence length": "78-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIJ517P4F", "file_type": "reads", "display_title": "4DNFIJ517P4F.fastq.gz", "paired_end": "1", "uuid": "810c60d1-fdcd-430f-b8b3-e355ae47d049", "@id": "/files-fastq/4DNFIJ517P4F/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIO5V7CGX/", "uuid": "c3e1d6cc-cb0b-4759-ab57-07735e9f087c", "upload_key": "c3e1d6cc-cb0b-4759-ab57-07735e9f087c/4DNFIO5V7CGX.fastq.gz", "file_type": "reads", "file_size": 1888128160, "accession": "4DNFIO5V7CGX", "display_title": "4DNFIO5V7CGX.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIO5V7CGX/@@download/4DNFIO5V7CGX.fastq.gz", "quality_metric": {"uuid": "b30c96c2-2a89-42e6-8994-9c592025ec5a", "Total Sequences": 27384069, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIO5V7CGX/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/b30c96c2-2a89-42e6-8994-9c592025ec5a/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIKCC6Y3I", "file_type": "reads", "display_title": "4DNFIKCC6Y3I.fastq.gz", "paired_end": "2", "uuid": "5c27d505-073f-47cc-ba84-6f48a54e73a3", "@id": "/files-fastq/4DNFIKCC6Y3I/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIKCC6Y3I/", "uuid": "5c27d505-073f-47cc-ba84-6f48a54e73a3", "upload_key": "5c27d505-073f-47cc-ba84-6f48a54e73a3/4DNFIKCC6Y3I.fastq.gz", "file_type": "reads", "file_size": 2234907982, "accession": "4DNFIKCC6Y3I", "display_title": "4DNFIKCC6Y3I.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIKCC6Y3I/@@download/4DNFIKCC6Y3I.fastq.gz", "quality_metric": {"uuid": "b7ba170d-fd88-439f-9102-e8edf121df7e", "Total Sequences": 27384069, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKCC6Y3I/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/b7ba170d-fd88-439f-9102-e8edf121df7e/", "Sequence length": "77-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIO5V7CGX", "file_type": "reads", "display_title": "4DNFIO5V7CGX.fastq.gz", "paired_end": "1", "uuid": "c3e1d6cc-cb0b-4759-ab57-07735e9f087c", "@id": "/files-fastq/4DNFIO5V7CGX/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIAQVL5BB/", "uuid": "48af3ecb-b4de-4378-8623-d90a5a31fa9d", "upload_key": "48af3ecb-b4de-4378-8623-d90a5a31fa9d/4DNFIAQVL5BB.fastq.gz", "file_type": "reads", "file_size": 1317194934, "accession": "4DNFIAQVL5BB", "display_title": "4DNFIAQVL5BB.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIAQVL5BB/@@download/4DNFIAQVL5BB.fastq.gz", "quality_metric": {"uuid": "d05d79b3-3792-43cd-8717-ffbd796a6a7d", "Total Sequences": 19101804, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAQVL5BB/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/d05d79b3-3792-43cd-8717-ffbd796a6a7d/", "Sequence length": "20-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIA3WTZDU", "file_type": "reads", "display_title": "4DNFIA3WTZDU.fastq.gz", "paired_end": "2", "uuid": "493a8bb5-d863-4c0e-bb3b-2ced0ef10812", "@id": "/files-fastq/4DNFIA3WTZDU/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_classification": "raw file", "notes_to_tsv": ["This fastq file has already had the barcode identification step of the SPRITE pipeline run on it. The SPRITE barcodes are now appended to the read ID lines, and the DPM adapter has been trimmed, resulting in a discrepancy of some read lengths between read 1 and 2 of each pair."], "@id": "/files-fastq/4DNFIA3WTZDU/", "uuid": "493a8bb5-d863-4c0e-bb3b-2ced0ef10812", "upload_key": "493a8bb5-d863-4c0e-bb3b-2ced0ef10812/4DNFIA3WTZDU.fastq.gz", "file_type": "reads", "file_size": 1550217760, "accession": "4DNFIA3WTZDU", "display_title": "4DNFIA3WTZDU.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "status": "released", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIA3WTZDU/@@download/4DNFIA3WTZDU.fastq.gz", "quality_metric": {"uuid": "a25b5285-c79f-4b43-a2b8-45df8c9c749d", "Total Sequences": 19101804, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIA3WTZDU/fastqc_report.html", "display_title": "QualityMetricFastqc from 2021-09-28", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/a25b5285-c79f-4b43-a2b8-45df8c9c749d/", "Sequence length": "79-151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIAQVL5BB", "file_type": "reads", "display_title": "4DNFIAQVL5BB.fastq.gz", "paired_end": "1", "uuid": "48af3ecb-b4de-4378-8623-d90a5a31fa9d", "@id": "/files-fastq/4DNFIAQVL5BB/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["guttman-lab:h1de-sprite-rep1"], "protocol": {"uuid": "ee9a8bff-ddf1-4066-acba-34ef431ac28a", "status": "released", "@id": "/protocols/ee9a8bff-ddf1-4066-acba-34ef431ac28a/", "display_title": "SPRITE_Protocol_DNA_January_2018.pdf", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXOU8O8X7", "biosample": {"@id": "/biosamples/4DNBSS8FXBVU/", "@type": ["Biosample", "Item"], "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "uuid": "3aec75ad-87dc-4f79-a7d5-837403e5a509", "display_title": "4DNBSS8FXBVU", "modifications_summary": "None", "biosample_type": "in vitro differentiated cells", "status": "released", "accession": "4DNBSS8FXBVU", "treatments_summary": "None", "biosource": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.wicell.org/home/stem-cell-lines/catalog-of-stem-cell-lines/wa01.cmsx", "award": {"status": "current", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "synonyms": ["animal stem cell"], "term_id": "CL:0000034", "display_title": "stem cell", "preferred_name": "stem cell", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:h1wa01T1", "4dn-dcic-lab:h1wa01T1"], "accession": "4DNSRV3SKQ8M", "cell_line": {"slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "synonyms": ["H1"], "term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "@type": ["OntologyTerm", "Item"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "display_title": "H1-hESC", "preferred_name": "H1-hESC", "term_name": "H1-hESC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"protected_data": false, "uuid": "c97775b7-3d00-4132-9598-863797b8ef14", "display_title": "4DNIN3RG3ZKE", "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNIN3RG3ZKE/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Homo sapiens male H1 embryonic stem cell (WA01)", "date_created": "2017-04-10T01:14:03.094143+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"@id": "/protocols/c0319394-33f9-4f4e-8e20-b3d413c4eed6/", "status": "released", "@type": ["Protocol", "Item"], "uuid": "c0319394-33f9-4f4e-8e20-b3d413c4eed6", "display_title": "4DN_H1_SOP-220126_2.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-08-29T13:33:38.896302+00:00"}, "modifications": [], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "biosource_vendor": {"display_title": "WiCell.org", "status": "released", "@type": ["Vendor", "Item"], "uuid": "41784f69-697d-42c2-82b1-b52bc5ea3519", "@id": "/vendors/wicellorg/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRV3SKQ8M/", "@type": ["Biosource", "Item"], "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "external_references": [], "biosource_name": "H1-hESC (Tier 1)", "biosource_category": ["H1-hESC", "Human stem cell"], "organism": {"@type": ["Organism", "Item"], "display_title": "H. sapiens", "status": "released", "name": "human", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "@id": "/badges/biosample-metadata-incomplete/", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "badge_classification": "Warning", "status": "released", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 11, "description": "DNA SPRITE on H1 (Tier 1) cells differentiated to definitive endoderm - biological replicate 1", "sop_mapping": {"has_sop": "No"}, "date_created": "2021-09-13T21:49:11.386800+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-09-11T14:38:03.935453+00:00"}, "public_release": "2024-09-11", "schema_version": "5", "experiment_type": {"@id": "/experiment-types/dna-sprite/", "uuid": "4004ae76-2f5c-42b6-9f72-488f60963f04", "status": "released", "title": "DNA SPRITE", "experiment_category": "Sequencing", "display_title": "DNA SPRITE", "assay_subclass_short": "Ligation-free 3C", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"display_title": "4DNFICGLAAD6.clusters.gz", "@type": ["FileProcessed", "File", "Item"], "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/484b3e11-ed3b-4882-be64-5a920ee276a3/4DNFICGLAAD6.clusters.gz", "file_type": "multi-contact read clusters", "upload_key": "484b3e11-ed3b-4882-be64-5a920ee276a3/4DNFICGLAAD6.clusters.gz", "href": "/files-processed/4DNFICGLAAD6/@@download/4DNFICGLAAD6.clusters.gz", "status": "released", "file_format": {"file_format": "clusters", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "e4696bdd-7a8f-44ee-ad69-1502061c5cf1", "display_title": "clusters", "@id": "/file-formats/clusters/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFICGLAAD6", "uuid": "484b3e11-ed3b-4882-be64-5a920ee276a3", "file_size": 377612265, "@id": "/files-processed/4DNFICGLAAD6/", "file_type_detailed": "multi-contact read clusters (clusters)", "file_classification": "processed file", "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA SPRITE", "experiment_bucket": "processed file", "dataset": "SPRITE on H1-DE cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Mitchell Guttman, CALTECH"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2021-09-29", "biosample_quantity": 5000.0, "fragment_size_range": "250-600", "fragmentation_method": "see protocol document", "average_fragment_size": 360, "biosample_quantity_units": "cells", "library_preparation_date": "2018-03-23", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-seq/4DNEXOU8O8X7/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "983caf01-dd6a-4fa6-aae6-7d12b7350eb9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DNA SPRITE on H1-hESC (Tier 1) differentiated to definitive endoderm - 4DNEXOU8O8X7", "external_references": [], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESO4YWG21/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "uuid": "59f9833e-0cdc-49cb-b89d-adeade0c1a1d", "display_title": "4DNESO4YWG21", "accession": "4DNESO4YWG21", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Default", "value": null}, "experiment_summary": "DNA SPRITE on H1-hESC (Tier 1) differentiated to definitive endoderm", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSS8FXBVU/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}