ExperimentSetReplicate

ExperimentSet4DNESI1DNSGF
released
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in situ Hi-C on PDX1-GFP idCAS9-KRAB H1 human embryonic stem cells differentiated to definitive endoderm (DE)

   May 31st, 2023 at 3:11pm
Source Publication
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.
Luo R, Yan J, et al., Nature genetics 2023

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
in vitro differentiated cells
Sample 
PDX1-eGFP dCAS9-KRAB H1 differentiated to definitive endoderm
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: Arima - A1, A2

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESI1DNSGF
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIIOEXLEY
214.54m
44.295%
28.475%
27.229%
Experiment
4DNEXNDOLHY1
Bio Rep 1, Tec Rep 1
in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to definitive endoderm with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFILKIVFHL
214.54m
44.295%
28.475%
27.229%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESI1DNSGF
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI8SNUTVY
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXNDOLHY1
Bio Rep 1, Tec Rep 1
in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to definitive endoderm with Arima - A1, A2
File
Alignments (bam)
4DNFIS86A8QJ
311.3m
8.286%
10.619%
3.825%
8.354%
0.201%