NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2233368 Query DataSets for GSM2233368
Status Public on Dec 01, 2016
Title Input
Sample type SRA
 
Source name 3T3-L1_Input
Organism Mus musculus
Characteristics cell line: 3T3-L1
cell type: Preadipocyte cell line
Treatment protocol Two days post confluency (day 0), 3T3-L1 cells were induced to differentiate using a standard cocktail of adipogenic inducers (dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and fetal bovine serum). Two days post induction (day 2), medium was changed to DMEM supplemented with fetal bovine serum and insulin. Cells were maintained in DMEM supplemented with fetal bovine serum for the remainder of the differentiation. For knock down experiments, pre-confluent 3T3-L1 cells were transduced 4 days before induction of differentiation by incubation for 24 hours at 37°C with medium containing lentiviral constructs (shKDM5A/B/C or control shLuc) and 6 μg/mL polybrene (Sigma). After 24 hours the medium was changed to normal growth medium.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed in 3T3-L1 cells essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
KDM5A ChIP-seq and matching Input tag counts were normalized to 10M reads using HOMER.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: H3K4me3_promoter_peaks_tags.txt: Table containing promoter H3K4me3 binding sites, including normalized tag counts for H3K4me3 libraries
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C libraries
RNA_all_genes_log2_tags_kb.txt: Table containing gene expression data for all RNA-seq libraries (reported as log2(tags/kb))
 
Submission date Jul 14, 2016
Last update date May 15, 2019
Contact name Ann-Sofie Bøgh 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
 
Platform ID GPL18480
Series (1)
GSE84410 The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation
Relations
BioSample SAMN05391983
SRA SRX1949145

Supplementary file Size Download File type/resource
GSM2233368_SM353_GCCAAT_Input_DSG.TD.bedgraph.gz 33.6 Mb (ftp)(http) BEDGRAPH
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