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GEO accession:
Series GSE196450
Query DataSets for GSE196450
Status
Public on Jul 28, 2023
Title
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Organism
Homo sapiens
Experiment type
Expression profiling by high throughput sequencing
Other
Summary
This SuperSeries is composed of the SubSeries listed below.
Overall design
Refer to individual Series
Web link
https://www.nature.com/articles/s41467-023-41316-4
Citation(s)
37726281
Submission date
Feb 09, 2022
Last update date
Oct 03, 2023
Contact name
Ryuichiro Nakato
E-mail(s)
rnakato@iqb.u-tokyo.ac.jp
Phone
+81-3-5841-1471
Organization name
The University of Tokyo
Department
Institute for Quantitative Biosciences
Lab
Laboratory of Computational Genomics
Street address
1-1-1 Yayoi
City
Bunkyo-ku
State/province
Tokyo
ZIP/Postal code
113-0032
Country
Japan
Platforms (3)
GPL16791
Illumina HiSeq 2500 (Homo sapiens)
GPL20795
HiSeq X Ten (Homo sapiens)
GPL30173
NextSeq 2000 (Homo sapiens)
Samples (126)
Less...
More...
GSM5858314
Hi-C siCTCF replicate1
GSM5858315
Hi-C siCTCF replicate2
GSM5858316
Hi-C siCTCF 72h
GSM5858317
Hi-C siCTCF 120h
GSM5858318
Hi-C siCTCF (si626 and si628 double)
GSM5858319
Hi-C Control replicate1
GSM5858320
Hi-C Control replicate2
GSM5858321
Hi-C Control replicate3
GSM5858322
Hi-C Control replicate4
GSM5858323
Hi-C Control replicate5
GSM5858324
Hi-C Control replicate6
GSM5858325
Hi-C siESCO1 replicate1
GSM5858326
Hi-C siESCO1 replicate2
GSM5858327
Hi-C JQ1(-)
GSM5858328
Hi-C JQ1(+)
GSM5858329
Hi-C siMau2
GSM5858330
Hi-C siNIPBL replicate1
GSM5858331
Hi-C siNIPBL replicate2
GSM5858332
Hi-C siNIPBL 24h
GSM5858333
Hi-C siNIPBL 48h
GSM5858334
Hi-C siNIPBL 72h
GSM5858335
Hi-C siNIPBL si8
GSM5858336
Hi-C siRad21 siNIPBL double
GSM5858337
Hi-C siPDS5A siPDS5B double
GSM5858338
Hi-C siPDS5A 48h
GSM5858339
Hi-C siPDS5A 72h
GSM5858340
Hi-C siPDS5B
GSM5858341
Hi-C siRad21 replicate1
GSM5858342
Hi-C siRad21 replicate2
GSM5858343
Hi-C siRad21 replicate3
GSM5858344
Hi-C siWAPL
GSM5884388
RNA-seq siRad21 replicate1
GSM5884389
RNA-seq siRad21 replicate2
GSM5884390
RNA-seq siCTCF replicate1
GSM5884391
RNA-seq siCTCF replicate2
GSM5884392
RNA-seq Control1 replicate1
GSM5884393
RNA-seq Control1 replicate2
GSM5884394
RNA-seq siRad21 48h replicate1
GSM5884395
RNA-seq siRad21 48h replicate2
GSM5884396
RNA-seq siNIPBL 48h replicate1
GSM5884397
RNA-seq siNIPBL 48h replicate2
GSM5884398
RNA-seq siNIPBL 72h replicate1
GSM5884399
RNA-seq siNIPBL 72h replicate2
GSM5884400
RNA-seq siNIPBL si8 replicate1
GSM5884401
RNA-seq siNIPBL si8 replicate2
GSM5884402
RNA-seq Control2 replicate1
GSM5884403
RNA-seq Control2 replicate2
GSM5884404
RNA-seq siWAPL replicate1
GSM5884405
RNA-seq siWAPL replicate2
GSM5884406
RNA-seq siRad21 siNIPBL double replicate1
GSM5884407
RNA-seq siRad21 siNIPBL double replicate2
GSM5884408
RNA-seq siPDS5A replicate1
GSM5884409
RNA-seq siPDS5A replicate2
GSM5884410
RNA-seq siPDS5A siPDS5B double replicate1
GSM5884411
RNA-seq siPDS5A siPDS5B double replicate2
GSM5884412
RNA-seq siPDS5B replicate1
GSM5884413
RNA-seq siPDS5B replicate2
GSM5884414
RNA-seq Control3 replicate1
GSM5884415
RNA-seq Control3 replicate2
GSM5884416
RNA-seq JQ1(+) replicate1
GSM5884417
RNA-seq JQ1(+) replicate2
GSM5884418
RNA-seq siESCO1 replicate1
GSM5884419
RNA-seq siESCO1 replicate2
GSM5884420
RNA-seq siMau2 replicate1
GSM5884421
RNA-seq siMau2 replicate2
GSM5899605
ChIP-seq CTCF Control replicate1
GSM5899606
ChIP-seq Mau2 Control replicate1
GSM5899607
ChIP-seq Rad21 Control replicate1
GSM5899608
ChIP-seq Input Control replicate1
GSM5899609
ChIP-seq Rad21 siRad21
GSM5899610
ChIP-seq Input siRad21 replicate1
GSM5899611
ChIP-seq CTCF siCTCF
GSM5899612
ChIP-seq Rad21 siCTCF
GSM5899613
ChIP-seq Input siCTCF
GSM5899614
ChIP-seq Mau2 siNIPBL
GSM5899615
ChIP-seq Rad21 siNIPBL
GSM5899616
ChIP-seq Input siNIPBL replicate1
GSM5899617
ChIP-seq Rad21 Control replicate2
GSM5899618
ChIP-seq Input Control replicate2
GSM5899619
ChIP-seq Rad21 siESCO1
GSM5899620
ChIP-seq Input siESCO1
GSM5899621
ChIP-seq CTCF Control replicate2
GSM5899622
ChIP-seq CTCF siESCO1
GSM5899623
ChIP-seq BRD4 JQ1(-)
GSM5899624
ChIP-seq Input JQ1(-)
GSM5899625
ChIP-seq BRD4 JQ1(+)
GSM5899626
ChIP-seq Input JQ1(+)
GSM5899627
ChIP-seq Smc3ac Control
GSM5899628
ChIP-seq Input (for Smc3ac)
GSM5899629
ChIP-seq H3K27ac Control
GSM5899630
ChIP-seq H3K27ac siNIPBL
GSM5899631
ChIP-seq H3K27ac siRad21
GSM5899632
ChIP-seq H3K36me3 Control
GSM5899633
ChIP-seq H3K36me3 siNIPBL
GSM5899634
ChIP-seq H3K36me3 siRad21
GSM5899635
ChIP-seq H3K4me3 Control
GSM5899636
ChIP-seq H3K4me3 siNIPBL
GSM5899637
ChIP-seq H3K4me3 siRad21
GSM5899638
ChIP-seq Input Control replicate3
GSM5899639
ChIP-seq Input siNIPBL replicate2
GSM5899640
ChIP-seq Input siRad21 replicate2
GSM5899641
ChIP-seq H3K27me3 Control
GSM5899642
ChIP-seq H3K27me3 siNIPBL
GSM5899643
ChIP-seq H3K27me3 siRad21
GSM5899644
ChIP-seq Input Control replicate5
GSM5899645
ChIP-seq Input siNIPBL replicate4
GSM5899646
ChIP-seq Input siRad21 replicate3
GSM5899647
ChIP-seq AFF4 siNIPBL
GSM5899648
ChIP-seq AFF4 Control
GSM5899649
ChIP-seq Pol2 siNIPBL
GSM5899650
ChIP-seq Pol2 Control
GSM5899651
ChIP-seq Pol2Ser2 siNIPBL
GSM5899652
ChIP-seq Pol2Ser2 Control
GSM5899653
ChIP-seq Input siNIPBL replicate3
GSM5899654
ChIP-seq Input Control replicate4
GSM5899655
ChIP-seq H3K4me2 siNIPBL
GSM5899656
ChIP-seq H3K4me2 Control
GSM5899657
ChIP-seq Med1 Control
GSM7011759
ChIP-seq H3K27ac siNIPBL replicate2
GSM7011760
ChIP-seq H3K27ac Control replicate2
GSM7011761
ChIP-seq H3K27me3 siNIPBL replicate2
GSM7011762
ChIP-seq H3K27me3 Control replicate2
GSM7011763
ChIP-seq H3K36me3 siNIPBL replicate2
GSM7011764
ChIP-seq H3K36me3 Control replicate2
GSM7011765
ChIP-seq Rad21 siNIPBL replicate2
GSM7011766
ChIP-seq Rad21 Control replicate3
This SuperSeries is composed of the following SubSeries:
GSE196034
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [Hi-C]
GSE196449
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [RNA-seq]
GSE196727
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [ChIP-seq]
Relations
BioProject
PRJNA804917
Download family
Format
SOFT formatted family file(s)
SOFT
MINiML formatted family file(s)
MINiML
Series Matrix File(s)
TXT
Supplementary file
Size
Download
File type/resource
GSE196450_RAW.tar
58.2 Gb
(http)
(custom)
TAR (of BED, BW, HIC, TXT)
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