ExperimentSetReplicate

ExperimentSet4DNESNGESP28
replaced

Mapping RNA-genome interactions in HFFc6 cell line using MARGI technology

   November 28th, 2018 at 10:20am

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: This Experiment Set Supersedes - 4DNESJC437VS  


This experiment set supercedes 4DNESJC437VS because new technical replicates were added.

Note: Replaced Item - 4DNESNGESP28  


This experiment set was replaced by 4DNES9Y1GHK4 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. Two of the technical replicates that corresponding to miseq QC runs have been removed and additional new sequencing replicates (i.e. new fastq files) have been added to each biological replicate experiment of the superseding replicate set. 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 
immortalized cells
Experiment Type(s) 
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: AluI

10 Processed Files

Experiment
File
File Type
File Size
From Multiple Experiments
4DNESNGESP28
Multiple Experiments
contact list-combined (pairs)
1.59 GB
contact matrix (mcool)
385.04 MB
Experiment
4DNEXRJN8UYK
Bio Rep 1, Tec Rep 3
MARGI on HFFc6 (Tier 1)
alignments (bam)
49.74 GB
contact list-replicate (pairs)
652.59 MB
Experiment
4DNEXLLYE3XZ
Bio Rep 1, Tec Rep 4
MARGI on HFFc6 (Tier 1)
alignments (bam)
53.3 GB
contact list-replicate (pairs)
931.82 MB
Experiment
4DNEXWXUC1X2
Bio Rep 1, Tec Rep 1
MARGI on HFFc6 (Tier 1)
alignments (bam)
4.34 GB
contact list-replicate (pairs)
91.62 MB
Experiment
4DNEX21WVKWL
Bio Rep 1, Tec Rep 2
MARGI on HFFc6 (Tier 1)
alignments (bam)
3.82 GB
contact list-replicate (pairs)
120.28 MB

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>200000)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESNGESP28
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI95SASIY
52.25m
7.467%
59.139%
33.394%
Experiment
4DNEXRJN8UYK
Bio Rep 1, Tec Rep 3
MARGI on HFFc6 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIXNEBP84
19.01m
6.868%
63.439%
29.693%
Experiment
4DNEXLLYE3XZ
Bio Rep 1, Tec Rep 4
MARGI on HFFc6 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIYN8SZ4V
27.35m
7.726%
56.855%
35.419%
Experiment
4DNEXWXUC1X2
Bio Rep 1, Tec Rep 1
MARGI on HFFc6 (Tier 1)
File
Contact List-replicate (pairs)
4DNFI3Z3CCKZ
2.56m
6.495%
62.831%
30.674%
Experiment
4DNEX21WVKWL
Bio Rep 1, Tec Rep 2
MARGI on HFFc6 (Tier 1)
File
Contact List-replicate (pairs)
4DNFILSC65AG
3.33m
9.502%
50.513%
39.985%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESNGESP28
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOPSHWAM
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000