ExperimentSetReplicate

ExperimentSet4DNESWFRUPLR
released
View JSON

Capture Hi-C on HAP-1 cells with inversion of region 1 B-forward CTCF site (biotin-ATP tag).

   April 10th, 2017 at 1:11am
Source Publication
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Sanborn AL, Rao SS, et al., Proceedings of the National Academy of Sciences of the United States of America 2015

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HAP-1
Experiment Type(s) 
Capture Hi-C
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Target: GRCh38:1:179830865-181830865 region, GRCh38:5:30999893-32999894 region, GRCh38:8:131987753-133987757 region

11 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESWFRUPLR
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI8B3YH87
4.39m
57.159%
15.097%
27.744%
Experiment
4DNEX8KPXKZE
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIQ5RZSXU
750.3k
58.261%
15.544%
26.195%
Experiment
4DNEXK179IOV
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI91S1U76
718.08k
58.635%
15.479%
25.885%
Experiment
4DNEXY744GG9
Bio Rep 1, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIUY2P7SH
1.72m
55.064%
14.123%
30.813%
Experiment
4DNEXU2KZRN9
Bio Rep 1, Tec Rep 4
Capture Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIV9QH4LQ
1.2m
58.589%
15.984%
25.427%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESWFRUPLR
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIR7WXURG
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
4DNEX8KPXKZE
Bio Rep 1, Tec Rep 1
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI979LF96
1.16m
6.525%
19.022%
4.657%
4.988%
1.659%
Experiment
4DNEXK179IOV
Bio Rep 1, Tec Rep 2
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIVSB1GQ3
1.09m
6.415%
18.452%
4.394%
4.669%
1.46%
Experiment
4DNEXY744GG9
Bio Rep 1, Tec Rep 3
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI55LRFQB
2.64m
6.61%
18.602%
4.654%
4.94%
1.053%
Experiment
4DNEXU2KZRN9
Bio Rep 1, Tec Rep 4
Capture Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIAJ685C3
1.8m
6.447%
17.662%
4.396%
4.695%
1.028%