NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE123398 Query DataSets for GSE123398
Status Public on May 01, 2019
Title Genome-wide analysis of pSTAT3 (Tyr705) in diffuse large B-cell lymphoma
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Diffuse large B cell lymphoma (DLBCL), the most common non-Hodgkin lymphoma, includes two main molecular subtypes: activated B cell-like (ABC) DLBCL and germinal center B cell-like (GCB) DLBCL. ABC DLBCL is more aggressive, with the activated JAK1-STAT3 pathway that promotes cell survival. In order to study the underlying pathogenic mechanism, we performed a ChIP-seq experiment by phospho-STAT3(Tyr705) antibody in ABC DLBCL cell lines, and identified 3,456 STAT3 target genes genome-wide. In parallel, ChIP-seq experiment was performed with STAT3 antibody in α-IgM stimulated naïve B cells for verification of these targets of STAT3 protein.
TMD8 was treated by eithor DMSO or AZD1480 (JAK inhibitor) for 4hrs, ChIP-seq experiments were performed by pSTAT3(Tyr705) antibody (#9145S, Cell signaling). Naïve B cells were collected from peripheral blood mononuclear cells by Naive B Cell Isolation kit (miltenyi biotec; 130-091-150), and treated by 10ug/ml α-IgM (southernbiotech; #2020-01) for 24hrs. ChIP-seq experiments were performed by STAT3 antibody (SC-482X, Santa Cruz).
 
Overall design TMD8 cells were treated by eithor DMSO or AZD1480(JAK inhibitor) for 4hrs. Naïve B cells were collected from peripheral blood mononuclear cells by Naive B Cell Isolation kit (miltenyi biotec; 130-091-150), and treated by 10ug/ml α-IgM (southernbiotech; #2020-01) for 24hrs.
 
Contributor(s) Rui L, Lu L
Citation(s) 30926771
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 CA187299 Epigenetic Gene Regulation by JAK1 Kinase in Diffuse Large B-Cell Lymphoma UNIVERSITY OF WISCONSIN MADISON Lixin Rui
Submission date Dec 06, 2018
Last update date Jul 31, 2019
Contact name Lixin Rui
E-mail(s) lrui@medicine.wisc.edu
Organization name Wisconsin Ins for Medical Res
Street address 1111 Highland ave, Room 4053
City Madison
State/province WI
ZIP/Postal code 53705
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM3502665 pSTAT3CHIP-TMD8-DMSO
GSM3502666 pSTAT3CHIP-TMD8-AZD1480
GSM3502667 STAT3CHIP-IGMNB
Relations
BioProject PRJNA508625
SRA SRP172690

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE123398_RAW.tar 519.0 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap