ExperimentSetReplicate

ExperimentSet4DNESN3CDATJ
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 short nuclei prep (Covaris truChIP™ Chromatin Shearing Kit, section B. Nuclei Preparation, steps 8-10) (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
4DNESN3CDATJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI2UM2XD6
15.51m
49.932%
33.288%
16.78%
Experiment
4DNEXHDQ3TJT
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIZ4HBDMJ
6.68m
49.395%
34.4%
16.205%
Experiment
4DNEXDAGKIDV
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFI1HM4ZSQ
8.82m
50.338%
32.445%
17.217%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESN3CDATJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIIQI3SSY
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
4DNEXHDQ3TJT
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Alignments (bam)
4DNFIXPZMBI4
11.73m
13.664%
10.905%
12.961%
5.474%
0.226%
Experiment
4DNEXDAGKIDV
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on GM12878 (Tier 1)
File
Alignments (bam)
4DNFIZS4YLAP
14.15m
13.37%
10.636%
8.702%
4.926%
0.189%