ExperimentSetReplicate

ExperimentSet4DNESI8KI62W
released
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HiC on WT ZF Embryos Collected at 4h post-fertilization , vehicle control DMSO

   June 18th, 2020 at 2:33pm
Source Publication
Chromatin architecture transitions from zebrafish sperm through early embryogenesis.
Wike CL, Guo Y, et al., Genome research 2021

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
D. rerio
Sample Type 
whole organisms
Sample 
Zebrafish Embryo
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

18 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESI8KI62W
Multiple Experiments
File
Contact List-combined (pairs)
4DNFICLAAEG7
193.08m
12.578%
73.36%
14.062%
Experiment
4DNEXDRCVL28
Bio Rep 1, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Contact List-replicate (pairs)
4DNFIDVL3KMU
11.73m
16.437%
61.099%
22.464%
Experiment
4DNEXKZS643D
Bio Rep 1, Tec Rep 2
in situ Hi-C on Zebrafish Embryo with MboI
File
Contact List-replicate (pairs)
4DNFI4FKY87E
34.05m
11.705%
71.926%
16.369%
Experiment
4DNEXTSJKHTV
Bio Rep 2, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Contact List-replicate (pairs)
4DNFIE8SPPYV
10.17m
30.932%
44.837%
24.231%
Experiment
4DNEXNQ2FUVV
Bio Rep 2, Tec Rep 2
in situ Hi-C on Zebrafish Embryo with MboI
File
Contact List-replicate (pairs)
4DNFIP8X13XA
29.95m
27.16%
51.012%
21.828%
Experiment
4DNEXQKA9QBM
Bio Rep 3, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Contact List-replicate (pairs)
4DNFIVQM3WA2
13.71m
25.269%
55.297%
19.433%
Experiment
4DNEXPPWG3ND
Bio Rep 4, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Contact List-replicate (pairs)
4DNFISFD2PXD
93.47m
3.881%
88.333%
7.786%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESI8KI62W
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI9O58861
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXDRCVL28
Bio Rep 1, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Alignments (bam)
4DNFI2RRVP19
26.11m
7.299%
16.039%
11.482%
20.266%
0.871%
Experiment
4DNEXKZS643D
Bio Rep 1, Tec Rep 2
in situ Hi-C on Zebrafish Embryo with MboI
File
Alignments (bam)
4DNFIUFR4N1W
218.06m
7.256%
12.179%
34.526%
30.424%
0.303%
Experiment
4DNEXTSJKHTV
Bio Rep 2, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Alignments (bam)
4DNFI9UT5B8I
27.28m
14.387%
14.788%
7.3%
26.241%
0.811%
Experiment
4DNEXNQ2FUVV
Bio Rep 2, Tec Rep 2
in situ Hi-C on Zebrafish Embryo with MboI
File
Alignments (bam)
4DNFIMXXXN93
251.78m
14.165%
11.402%
26.926%
35.613%
0.259%
Experiment
4DNEXQKA9QBM
Bio Rep 3, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Alignments (bam)
4DNFIMMMRBXD
39.61m
17.574%
12.398%
2.067%
33.338%
0.737%
Experiment
4DNEXPPWG3ND
Bio Rep 4, Tec Rep 1
in situ Hi-C on Zebrafish Embryo with MboI
File
Alignments (bam)
4DNFIW4YPH47
191.56m
3.942%
21.709%
20.598%
4.956%
0.94%