Information
Accession GMS-65-1 

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Submit date2022-01-31 12:21:48
Last update date2023-01-11 15:55:23
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
Sharing
Total file size4.32 GB
Keywords Chromatin  PHi-C  Hi-C 
 Study
Experiment type Hi-C experiment with mouse ESCs.PHi-C structure modeling.
Summary Public datasets were used.
Citation(s)
 Experiment
OrganismMouse
Cell (Tissue) mESCs
Protocol
Data processing HiCExplorer — HiCExplorer 3.7.2 documentation
 Analysis
[1]
H1 cell line (SRR2977621)
Browse  (All Tracks)
H1_human_RNA.bam (429.08 MB)
Human (hg38); RNA-Seq

BAM

[2]
Transcriptome at E16.5
Browse  (All Tracks)
E16.5_Rep1.bam (558.05 MB)
Mouse (mm10); RNA-Seq

BAM

[3]
Mouse ESC RNA-seq (GSM4647545)
Browse  
ESC1_RNA.bam (1.65 GB)
Mouse (mm10); RNA-Seq

BAM

[4]
Intra-chromosomal Hi-C contacts (mESC Rep1)
Browse  
mESC1.intra.hic (1.69 GB)
Mouse (mm10); Hi-C

HiC

 mCool  Cooler-Tree



PHi-C2 (polymer dynamics modeling)
chr1:113073000-120292000
(25Kb resolution, KR, 289 bins)

chr1:113073000-125292000
(25Kb resolution, KR, 489 bins)

chr1:113073000-125392000
(25Kb resolution, KR, 493 bins)

chr1:113073000-1254292000
(25Kb resolution, KR, 45649 bins)
failed

chr1:113073000-126292000
(25Kb resolution, KR, 529 bins)
failed

chr1:68130104-95278988
(50Kb resolution, KR, 543 bins)

chr3:33379052-35381277
(25Kb resolution, KR, 81 bins)

chr6:120331269-125153871
(25Kb resolution, KR, 193 bins)

chr8:104001214-123401213
(50Kb resolution, KR, 388 bins)

 Supplements
H1_human_RNA.bam
 H1 cell line (SRR2977621)
 application/octet-stream 429.08 MB MD5: ac69edf8538390c4bd1ed9fca4626ebd
E16.5_Rep1.bam
 Transcriptome at E16.5
 application/octet-stream 558.05 MB MD5: 4e3099b4c10f7719b321b0fe982c7224
ESC1_RNA.bam
 Mouse ESC RNA-seq (GSM4647545)
 application/octet-stream 1.65 GB MD5: 71958136fa9af43d30d25754b85399dc
mESC1.intra.hic
 Intra-chromosomal Hi-C contacts (mESC Rep1)
 application/octet-stream 1.69 GB MD5: 1c07ac5d23e49a94a82fdd46e7547738