ExperimentSetReplicate

ExperimentSet4DNESWST3UBH
released
View JSON

MicroC Libraries from HFFc6 cells with 3 biological replicates, FA and DSG cross-linked, MNase digestion

   December 10th, 2019 at 10:47pm
Source Publication
Ultrastructural Details of Mammalian Chromosome Architecture.
Krietenstein N, Abraham S, et al., Molecular cell 2020

Note: Superseding Item - 4DNESWST3UBH  

This experiment set supersedes 4DNESYTWHUH6 and 4DNESCZJD9KK because new biological replicates were added.

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HFFc6 (Tier 1)
Experiment Type(s) 
Micro-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MNase

40 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESWST3UBH
Multiple Experiments
File
Contact List-combined (pairs)
4DNFINYO612N
5.86 billion
19.212%
68.099%
12.69%
Experiment
4DNEXC1TYVLD
Bio Rep 1, Tec Rep 1
Micro-C on HFFc6 (Tier 1) with MNase
File
Contact List-replicate (pairs)
4DNFICOEXGPJ
499.96m
19.172%
74.271%
6.557%
Experiment
4DNEX1MDLILR
Bio Rep 1, Tec Rep 2
Micro-C on HFFc6 (Tier 1) with MNase
File
Contact List-replicate (pairs)
4DNFIK8UIB5B
521.09m
19.403%
73.939%
6.658%
Experiment
4DNEXRJYVOZJ
Bio Rep 1, Tec Rep 3
Micro-C on HFFc6 (Tier 1) with MNase
File
Contact List-replicate (pairs)
4DNFIYBTHGNA
496.69m
20.103%
74.055%
5.842%
Experiment
4DNEXONC5BJ1
Bio Rep 1, Tec Rep 4
Micro-C on HFFc6 (Tier 1) with MNase
File
Contact List-replicate (pairs)
4DNFIJZDEIZ3
512.44m
19.489%
74.539%
5.972%
Experiment
4DNEX9TF73VI
Bio Rep 1, Tec Rep 5
Micro-C on HFFc6 (Tier 1) with MNase
File
Contact List-replicate (pairs)
4DNFIN7IIIY6
502.97m
19.349%
73.91%
6.741%
Experiment
4DNEX5F27GL2
Bio Rep 1, Tec Rep 6
Micro-C on HFFc6 (Tier 1) with MNase
File
Contact List-replicate (pairs)
4DNFIBHI5YI9
516.55m
19.524%
74.466%
6.011%
Show 11 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESWST3UBH
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI9FVHJZQ
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXC1TYVLD
Bio Rep 1, Tec Rep 1
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFINB1CUQU
746.16m
3.502%
20.966%
8.522%
0.005%
0.072%
Experiment
4DNEX1MDLILR
Bio Rep 1, Tec Rep 2
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFINJ8BBBJ
743.86m
3.157%
20.913%
5.871%
0.007%
0.074%
Experiment
4DNEXRJYVOZJ
Bio Rep 1, Tec Rep 3
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFIHF468MZ
706.29m
3.245%
19.462%
6.966%
0.004%
0.075%
Experiment
4DNEXONC5BJ1
Bio Rep 1, Tec Rep 4
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFI44CAKN7
742.73m
3.53%
19.702%
7.768%
0.005%
0.075%
Experiment
4DNEX9TF73VI
Bio Rep 1, Tec Rep 5
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFIO9G2R18
735.11m
3.414%
20.267%
7.892%
0.006%
0.078%
Experiment
4DNEX5F27GL2
Bio Rep 1, Tec Rep 6
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFI1VMSHH3
729.68m
3.932%
19.998%
5.273%
0.006%
0.082%
Experiment
4DNEXY8QQ4GB
Bio Rep 2, Tec Rep 1
Micro-C on HFFc6 (Tier 1) with MNase
File
Alignments (bam)
4DNFI67GP12Q
342.66m
16.328%
20.682%
15.791%
0.003%
0.13%
Show 10 More