ExperimentSetReplicate

ExperimentSet4DNES14CNC1I
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Micro-C on JM8.N4 WT

   May 29th, 2019 at 6:06pm
Source Publication
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.
Hsieh TS, Cattoglio C, et al., Molecular cell 2020

Note on Processed Files  

Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
JM8.N4 (Tier 2)
Experiment Type(s) 
Micro-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: MNase

82 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES14CNC1I
Multiple Experiments
File
Contact List-combined (pairs)
4DNFILZ1CPT8
3.18 billion
29.035%
63.723%
7.242%
Experiment
4DNEXE6JLOZ9
Bio Rep 1, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Contact List-replicate (pairs)
4DNFI7PMIMNU
34.45m
0.328%
98.043%
1.629%
Experiment
4DNEXIJH8TEM
Bio Rep 2, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Contact List-replicate (pairs)
4DNFIA75O2OQ
31.94m
0.234%
98.257%
1.509%
Experiment
4DNEXNEHQ5BL
Bio Rep 3, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Contact List-replicate (pairs)
4DNFI1NWE5NA
31.9m
0.321%
98.238%
1.441%
Experiment
4DNEXTWJ3C6G
Bio Rep 4, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Contact List-replicate (pairs)
4DNFIBJO1PO3
29.12m
0.303%
97.851%
1.846%
Experiment
4DNEXQ8QZFUT
Bio Rep 5, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Contact List-replicate (pairs)
4DNFI21MGUG2
11.18m
16.29%
55.73%
27.98%
Experiment
4DNEXQZC9BBJ
Bio Rep 6, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Contact List-replicate (pairs)
4DNFIREWRYKA
7.73m
3.689%
88.359%
7.951%
Show 32 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES14CNC1I
Multiple Experiments
File
Contact Matrix (mcool)
4DNFINNZDDXV
50000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXE6JLOZ9
Bio Rep 1, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFIFM6AZEY
48.9m
2.009%
17.854%
8.722%
0.977%
0.095%
Experiment
4DNEXIJH8TEM
Bio Rep 2, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFIL8SOVBC
44.66m
1.971%
18.382%
7.204%
0.934%
0.099%
Experiment
4DNEXNEHQ5BL
Bio Rep 3, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFISPB2EYA
44.87m
2.243%
17.911%
7.876%
0.881%
0.094%
Experiment
4DNEXTWJ3C6G
Bio Rep 4, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFI7B5DIJA
41.33m
2.204%
18.956%
7.385%
1.009%
0.102%
Experiment
4DNEXQ8QZFUT
Bio Rep 5, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFI25TWG4P
15.52m
3.084%
21.408%
1.547%
1.928%
0.124%
Experiment
4DNEXQZC9BBJ
Bio Rep 6, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFINTOF73G
9.99m
2.513%
18.23%
1.003%
0.938%
0.119%
Experiment
4DNEX8WZ42US
Bio Rep 7, Tec Rep 1
Micro-C on JM8.N4 (Tier 2) with MNase
File
Alignments (bam)
4DNFIQQ9W3YQ
30.18m
1.873%
22.523%
17.223%
1.475%
0.088%
Show 31 More