|
| Status |
Public on Sep 03, 2019 |
| Title |
NSD2 overexpression links drives clustered chromatin and transcriptional changes in a subset of insulated domains of insulated domains |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We analyzed the impact of NSD2 overexpression on 3D genome reorganization and gene expression in multiple myeloma cell lines
|
| |
|
| Overall design |
RNAseq, ChIP-seq, Hi-C and HiChIP in multiple myeloma cell lines
|
| |
|
| Contributor(s) |
Lhoumaud P, Skok J |
| Citation(s) |
31649247 |
| |
| Submission date |
May 22, 2019 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Priscillia Lhoumaud |
| E-mail(s) |
Priscillia.Lhoumaud@nyumc.org
|
| Phone |
2122630503
|
| Organization name |
NYU Langone Health
|
| Department |
Pathology
|
| Lab |
Jane Skok
|
| Street address |
550 first avenue Smilow 307
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (48)
|
|
| Relations |
| BioProject |
PRJNA544287 |
| SRA |
SRP199225 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE131651_HiChIP_HIGH_CTCF.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE131651_HiChIP_LOW_CTCF.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE131651_NSD2_HIGH_arima.hic |
866.6 Mb |
(ftp)(http) |
HIC |
| GSE131651_NSD2_HIGH_compartments.bedGraph.gz |
769.1 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE131651_NSD2_HIGH_domains.k_001.bed.gz |
22.3 Kb |
(ftp)(http) |
BED |
| GSE131651_NSD2_HIGH_filtered_Acompartments.bed.gz |
7.4 Kb |
(ftp)(http) |
BED |
| GSE131651_NSD2_HIGH_filtered_Bcompartments.bed.gz |
7.3 Kb |
(ftp)(http) |
BED |
| GSE131651_NSD2_LOW_arima.hic |
903.5 Mb |
(ftp)(http) |
HIC |
| GSE131651_NSD2_LOW_compartments.bedGraph.gz |
769.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE131651_NSD2_LOW_domains.k_001.bed.gz |
21.1 Kb |
(ftp)(http) |
BED |
| GSE131651_NSD2_LOW_filtered_Acompartments.bed.gz |
9.8 Kb |
(ftp)(http) |
BED |
| GSE131651_NSD2_LOW_filtered_Bcompartments.bed.gz |
9.7 Kb |
(ftp)(http) |
BED |
| GSE131651_NTKOCTCF_new.hic |
143.1 Mb |
(ftp)(http) |
HIC |
| GSE131651_NTKO_CTCF_merged_ChIP_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE131651_RAW.tar |
3.2 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BW, TXT) |
| GSE131651_TKOCTCF_new.hic |
159.8 Mb |
(ftp)(http) |
HIC |
| GSE131651_TKO_CTCF_merged_ChIP_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE131651_ntkoCTCF.common.loops.sig.arc.format.txt.gz |
32.3 Kb |
(ftp)(http) |
TXT |
| GSE131651_tkoCTCF.common.loops.sig.arc.format.txt.gz |
32.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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