ExperimentSetReplicate

ExperimentSet4DNESFSCP5L8
released

in situ Hi-C on human embryonic stem cells (H1) - Control

   July 1st, 2021 at 5:48pm

Assay Description  


Note: Superseding Item - 4DNESFSCP5L8  


This experiment set supersedes 4DNESTCJSP7W because the replicate structure of the old set was determined to be incorrect as submitted. Experiments submitted as technical replicates were in fact biological replicates. A new biological replicate has been added to the superseding set and new sequencing replicates (i.e. new fastq files) have also been added to one of the superseded replicate experiments. Due to the change in replicate structure new accessions have been assigned for experiments and biosamples, however, accessions for unchanged files are shared between the new and replaced replicate sets..


Experiment Set Properties  


Set Type 
Replicate
Organism 
Sample Type 
stem cells
Experiment Type(s) 
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: Arima - A1, A2

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESFSCP5L8
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI5IL13WK
421.07m
57.531%
21.732%
20.737%
Experiment
4DNEX2T7JZ1O
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFI5M6BXPO
204.53m
54.615%
22.339%
23.046%
Experiment
4DNEXA1ATIBI
Bio Rep 2, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFIA3TKHP5
216.55m
60.285%
21.16%
18.556%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESFSCP5L8
Multiple Experiments
File
Contact Matrix (mcool)
4DNFICRGVN5L
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX2T7JZ1O
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Alignments (bam)
4DNFIHZVCVTB
315.96m
9.916%
11.62%
3.399%
10.333%
0.261%
Experiment
4DNEXA1ATIBI
Bio Rep 2, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Alignments (bam)
4DNFIDXKJB55
300.66m
7.404%
10.575%
1.587%
8.41%
0.194%