ExperimentSetReplicate

ExperimentSet4DNESMBE39SA
released
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Low sequencing coverage replicates of H3K4me3 PLAC-seq on GM12878 cells for parameter testing - 0.3% SDS in 1xNebuffer2, 42ºC, 10 min (Step 12 in protocol) and Covaris nuclei prep (Covaris truChIP™ Chromatin Shearing Kit, section B. Nuclei Preparation, step 1-10) (Step 30 in protocol)

   November 14th, 2019 at 8:04pm

Data Usage Guidelines  

Data Use Guidelines: This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper (doi:10.1038/nature23884) and the 4DN Data Portal paper (doi:10.1038/s41467-022-29697-4), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the Data Coordination and Integration Center.

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM12878 (Tier 1)
Experiment Type(s) 
PLAC-seq
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K4me3

7 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESMBE39SA
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIZW8AAG9
14.38m
50.979%
32.755%
16.266%
Experiment
4DNEX4YJM3RI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIGBBWF8V
6.52m
50.673%
33.079%
16.249%
Experiment
4DNEX398D42A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIP4X6QZK
7.86m
51.233%
32.487%
16.28%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESMBE39SA
Multiple Experiments
File
Contact Matrix (mcool)
4DNFILXPPI6D
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX4YJM3RI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Alignments (bam)
4DNFI3ZQR4Q2
10.48m
13.419%
11.09%
7.726%
5.624%
0.283%
Experiment
4DNEX398D42A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Alignments (bam)
4DNFIYCKOHHI
12.6m
13.066%
10.841%
8.744%
4.954%
0.202%