ExperimentSetReplicate

ExperimentSet4DNESTCJSP7W
replaced

Mapping RNA-genome interactions in H1 cell line using MARGI technology

   November 27th, 2018 at 2:37am

Data Usage Guidelines  


Data Use Guidelines: This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper (doi:10.1038/nature23884) and the 4DN Data Portal paper (doi:10.1038/s41467-022-29697-4), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the Data Coordination and Integration Center.

Assay Description  


Note: Replaced Item - 4DNESTCJSP7W  


This experiment set was replaced by 4DNESFSCP5L8 because the replicate structure of the old set was determined to be incorrect as submitted. Experiments submitted as technical replicates were in fact biological replicates. A new biological replicate has been added to the superseding set and new sequencing replicates (i.e. new fastq files) have also been added to one of the superseded replicate experiments. Due to the change in replicate structure new accessions have been assigned for experiments and biosamples, however, accessions for unchanged files are shared between the new and replaced replicate sets..


Experiment Set Properties  


Set Type 
Replicate
Organism 
Sample Type 
stem cells
Experiment Type(s) 
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: AluI

8 Processed Files

Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESTCJSP7W
Multiple Experiments
contact list-combined (pairs)
2.49 GB
-
contact matrix (mcool)
810.24 MB
Experiment
4DNEXJG75QSO
Bio Rep 1, Tec Rep 1
MARGI on H1-hESC (Tier 1)
alignments (bam)
59.5 GB
-
contact list-replicate (pairs)
1006.18 MB
-
Experiment
4DNEXUUUTV7X
Bio Rep 1, Tec Rep 2
MARGI on H1-hESC (Tier 1)
alignments (bam)
60.42 GB
-
contact list-replicate (pairs)
1.11 GB
-
Experiment
4DNEXKCVV4IB
Bio Rep 1, Tec Rep 3
MARGI on H1-hESC (Tier 1)
alignments (bam)
62.7 GB
-
contact list-replicate (pairs)
652.05 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>200000)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESTCJSP7W
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIC6UCT2X
76.1m
13.242%
30.997%
55.762%
Experiment
4DNEXJG75QSO
Bio Rep 1, Tec Rep 1
MARGI on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFIZZLJKSX
27.2m
12.8%
26.348%
60.851%
Experiment
4DNEXUUUTV7X
Bio Rep 1, Tec Rep 2
MARGI on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFICWA1X9Z
31.27m
14.763%
30.736%
54.501%
Experiment
4DNEXKCVV4IB
Bio Rep 1, Tec Rep 3
MARGI on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFIC9B8VE9
17.62m
11.223%
38.634%
50.143%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESTCJSP7W
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIWSIJ2SQ
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000