ExperimentSetReplicate

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ExperimentSet4DNESMU2MA2G
released
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Replicates of Hi-C on H9 hESC cells , containing a MYL2-H2B-GFP marker for cardiocytes, at day 7 differentiation - cardiac progenitor cell.

   August 7th, 2019 at 5:53pm
Source Publication
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells.
Zhang Y, Li T, et al., Nature genetics 2019

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
in vitro differentiated cells
Sample 
H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MboI

10 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESMU2MA2G
Multiple Experiments
File
4DNFIFKTOWQL
contact list-combined (pairs)
42.98 GB
-
File
4DNFIEJEFCAM
contact matrix (hic)
14.47 GB
-
File
4DNFIPO1DGLH
contact matrix (mcool)
10.21 GB
File
4DNFI9JHUI2I
boundaries (bed)
148.53 kB
-
File
4DNFIQRP1XKH
insulation score-diamond (bw)
8.05 MB
-
File
4DNFISPMZ3RU
compartments (bw)
205.68 kB
-
Experiment
4DNEXCUGCHE3
Bio Rep 1, Tec Rep 1
in situ Hi-C on H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast with MboI
File
4DNFIZ5PUTL4
alignments (bam)
307.21 GB
-
File
4DNFIMF8MCIC
contact list-replicate (pairs)
23.9 GB
-
Experiment
4DNEXIKZZCZH
Bio Rep 2, Tec Rep 1
in situ Hi-C on H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast with MboI
File
4DNFI62NONMM
alignments (bam)
302.91 GB
-
File
4DNFIAWN1IXC
contact list-replicate (pairs)
23.61 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESMU2MA2G
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIFKTOWQL
2.32 billion
55.232%
18.136%
26.633%
Experiment
4DNEXCUGCHE3
Bio Rep 1, Tec Rep 1
in situ Hi-C on H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast with MboI
File
Contact List-replicate (pairs)
4DNFIMF8MCIC
1.16 billion
52.824%
17.828%
29.348%
Experiment
4DNEXIKZZCZH
Bio Rep 2, Tec Rep 1
in situ Hi-C on H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast with MboI
File
Contact List-replicate (pairs)
4DNFIAWN1IXC
1.15 billion
57.655%
18.446%
23.9%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESMU2MA2G
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIPO1DGLH
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXCUGCHE3
Bio Rep 1, Tec Rep 1
in situ Hi-C on H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast with MboI
File
Alignments (bam)
4DNFIZ5PUTL4
1.88 billion
8.207%
11.632%
13.226%
5.065%
0.1%
Experiment
4DNEXIKZZCZH
Bio Rep 2, Tec Rep 1
in situ Hi-C on H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle myoblast with MboI
File
Alignments (bam)
4DNFI62NONMM
1.86 billion
8.051%
11.461%
13.404%
4.872%
0.098%