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Series GSE84410 Query DataSets for GSE84410
Status Public on Dec 01, 2016
Title The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Here we have characterized the role of KDM5 family during adipocyte differentiation of 3T3-L1 preadipocytes. Notably, our study represents the first to simultaneously knock down all the KDM5 family members thereby avoiding interference from redundancy between KDM5 subtypes. Using a combination of knockdown and genome-wide ChIP-seq and RNA-seq analyses we uncover the underlying mechanisms of the inhibition of adipogenesis as well as basic aspects of KDM5 function.
 
Overall design Genome-wide profiling of KDM5A binding in 3T3-L1 preadipocytes and differentiating adipocytes, and profiling of H3K4me3 and gene expression in 3T3-L1 cells depleted for KDM5 family members
 
Contributor(s) Brier AB, Loft A, Madsen JS, Rosengren T, Nielsen R, Schmidt SF, Liu Z, Yan Q, Gronemeyer H, Mandrup S
Citation(s) 27899593
Submission date Jul 14, 2016
Last update date May 15, 2019
Contact name Ann-Sofie B√łgh Brier
E-mail(s) a.boegh@me.com
Phone +4522969284
Organization name University of Southern Denmark, Odense
Department Department of Biochemistry and Molecular Biology
Lab Mandrup lab
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (34)
GSM2233343 RNA shLuc Day 0 exp 1
GSM2233344 RNA shLuc 4 hour exp 1
GSM2233345 RNA shLuc Day 2 exp 1
Relations
BioProject PRJNA329107
SRA SRP078506

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
GSE84410_H3K4me3_promoter_peaks_tags.txt.gz 705.0 Kb (ftp)(http) TXT
GSE84410_KDM5A_all_peaks_tags.txt.gz 3.5 Mb (ftp)(http) TXT
GSE84410_KDM5C_all_peaks_tags.txt.gz 478.3 Kb (ftp)(http) TXT
GSE84410_RAW.tar 735.9 Mb (http)(custom) TAR (of BEDGRAPH)
GSE84410_RNA_all_genes_log2_tags_kb.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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