ExperimentSetReplicate

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ExperimentSet4DNESQBZ6L8Z
released

TrAC-loop on H1 Tier1 cells- 4 biological replicates

   February 9th, 2018 at 4:05pm

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.


Experiment Set Properties  


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

11 Processed Files

Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESQBZ6L8Z
Multiple Experiments
contact list-combined (pairs)
2.78 GB
-
contact matrix (hic)
849.45 MB
-
contact matrix (mcool)
731 MB
Experiment
4DNEXCZUE2D9
Bio Rep 1, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
alignments (bam)
12.28 GB
-
contact list-replicate (pairs)
953.12 MB
-
Experiment
4DNEX9Q3KJG8
Bio Rep 2, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
alignments (bam)
12.49 GB
-
contact list-replicate (pairs)
870.76 MB
-
Experiment
4DNEXWL452NZ
Bio Rep 3, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
alignments (bam)
10.45 GB
-
contact list-replicate (pairs)
592.82 MB
-
Experiment
4DNEX37BWPZT
Bio Rep 4, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
alignments (bam)
10.3 GB
-
contact list-replicate (pairs)
692.33 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESQBZ6L8Z
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIWRDI1OS
176.89m
8.757%
81.84%
9.403%
Experiment
4DNEXCZUE2D9
Bio Rep 1, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFIP14P3DA
52.98m
11.647%
75.999%
12.355%
Experiment
4DNEX9Q3KJG8
Bio Rep 2, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFILGYM2LC
49.51m
9.246%
82.347%
8.408%
Experiment
4DNEXWL452NZ
Bio Rep 3, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFIPO3B1PB
34.26m
6.106%
85.514%
8.38%
Experiment
4DNEX37BWPZT
Bio Rep 4, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Contact List-replicate (pairs)
4DNFIER3LJY8
40.14m
6.603%
85.791%
7.606%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESQBZ6L8Z
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI1X7OG51
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXCZUE2D9
Bio Rep 1, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Alignments (bam)
4DNFI6Q46USR
183.46m
2.793%
22.336%
45.99%
0.004%
1.423%
Experiment
4DNEX9Q3KJG8
Bio Rep 2, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Alignments (bam)
4DNFIAPBQGI6
201.28m
2.954%
20.921%
51.523%
0.005%
0.919%
Experiment
4DNEXWL452NZ
Bio Rep 3, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Alignments (bam)
4DNFIV9TCZVO
189.46m
5.571%
17.163%
59.18%
0.003%
0.577%
Experiment
4DNEX37BWPZT
Bio Rep 4, Tec Rep 1
TrAC-loop on H1-hESC (Tier 1)
File
Alignments (bam)
4DNFIDFYYXZS
166.86m
5.134%
17.957%
52.849%
0.003%
0.709%