Experiment Set

4DNES1NCTCB9
released
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HAP-1 wild-type in situ Hi-C - a collection of experiments on unmodified wild-type HAP-1 haploid cells used to generate a base Hi-C map for this cell type.

   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

Assay Description  

Experiment Set Properties  

Set Type 
Custom
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HAP-1
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

10 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEX5NCT8WI
in situ Hi-C on HAP-1 with MboI
File
4DNFIHBBU3RC
alignments (bam)
40.86 GB
File
4DNFIWO14LYW
contact list-replicate (pairs)
2.76 GB
Experiment
4DNEXN16TEZZ
in situ Hi-C on HAP-1 with MboI
File
4DNFI97YJKKH
alignments (bam)
47.27 GB
File
4DNFIMYACUIM
contact list-replicate (pairs)
2.48 GB
Experiment
4DNEXASVIO87
in situ Hi-C on HAP-1 with MboI
File
4DNFI5MQUCRI
alignments (bam)
46.46 GB
File
4DNFISQCBGL1
contact list-replicate (pairs)
2.42 GB
Experiment
4DNEXHSQ1DTV
in situ Hi-C on HAP-1 with MboI
File
4DNFICQ95BOP
alignments (bam)
46.15 GB
File
4DNFI4Y4Z7AF
contact list-replicate (pairs)
3.7 GB
Experiment
4DNEXLZJN8LZ
in situ Hi-C on HAP-1 with MboI
File
4DNFIKWPZ4U5
alignments (bam)
45.3 GB
File
4DNFI2HTENAI
contact list-replicate (pairs)
2.85 GB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX5NCT8WI
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIHBBU3RC
224.54m
16.179%
11.235%
0.772%
7.71%
0.449%
Experiment
4DNEXN16TEZZ
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI97YJKKH
181.31m
6.293%
8.481%
2.999%
7.818%
0.267%
Experiment
4DNEXASVIO87
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFI5MQUCRI
179.26m
6.315%
8.765%
3.072%
8.141%
0.35%
Experiment
4DNEXHSQ1DTV
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFICQ95BOP
270.22m
6.829%
12.202%
1.425%
7.847%
0.531%
Experiment
4DNEXLZJN8LZ
in situ Hi-C on HAP-1 with MboI
File
Alignments (bam)
4DNFIKWPZ4U5
240.46m
18.632%
11.136%
0.843%
8.02%
0.474%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
Experiment
4DNEX5NCT8WI
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIWO14LYW
143.94m
50.786%
31.578%
17.636%
Experiment
4DNEXN16TEZZ
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFIMYACUIM
134.91m
60.974%
23.586%
15.439%
Experiment
4DNEXASVIO87
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFISQCBGL1
132.13m
58.775%
26.644%
14.581%
Experiment
4DNEXHSQ1DTV
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI4Y4Z7AF
193.74m
51.097%
31.157%
17.747%
Experiment
4DNEXLZJN8LZ
in situ Hi-C on HAP-1 with MboI
File
Contact List-replicate (pairs)
4DNFI2HTENAI
147.57m
51.856%
30.956%
17.188%