ExperimentSetReplicate

ExperimentSet4DNES7ODZ4MZ
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in situ Hi-C on 24 hour activated B cells, treated with flavopiridol (4 hour) to inhibit transcription

   November 27th, 2018 at 6:26pm
Source Publication
The Energetics and Physiological Impact of Cohesin Extrusion.
Vian L, Pekowska A, et al., Cell 2018

Assay Description  

Note on Processed Files  

Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
primary cells
Sample 
B cell derived cell line
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

36 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES7ODZ4MZ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIRREEHED
1.2 billion
57.002%
17.674%
25.324%
Experiment
4DNEXRQPAEQK
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIFS47MR1
66.32m
57.776%
19.486%
22.737%
Experiment
4DNEXOO6SD28
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI6LM3EMI
76.57m
57.128%
20.055%
22.817%
Experiment
4DNEXOYOGGZA
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIKW5S7K9
3.41k
53.97%
17.14%
28.89%
Experiment
4DNEXDS6Z21V
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI1GPFPVP
65.86m
56.355%
19.872%
23.773%
Experiment
4DNEXG9PCRZT
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIVMBUAL1
73.59m
57.729%
18.109%
24.162%
Experiment
4DNEX279YP3H
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFILZ2DVEL
67.1m
57.398%
14.294%
28.308%
Show 9 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES7ODZ4MZ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI3QLT3KJ
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXRQPAEQK
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI7RHOYHJ
93.68m
4.827%
11.754%
5.728%
6.892%
0.115%
Experiment
4DNEXOO6SD28
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFITW3X45W
108.29m
4.83%
11.305%
5.648%
7.503%
0.112%
Experiment
4DNEXOYOGGZA
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFID3MOU7A
13.38k
59.345%
4.418%
0.105%
10.616%
0.075%
Experiment
4DNEXDS6Z21V
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI9WD6YID
93.14m
4.789%
11.781%
5.825%
6.9%
0.121%
Experiment
4DNEXG9PCRZT
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFITQ5ZXNM
105.34m
5.588%
11.61%
5.59%
7.348%
0.114%
Experiment
4DNEX279YP3H
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIR5NXRG9
95.75m
4.906%
11.825%
5.47%
7.719%
0.139%
Experiment
4DNEXGH69W5N
Bio Rep 7, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI3STKK6N
101.62m
5.91%
11.64%
7.52%
7.101%
0.144%
Show 8 More