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Sample GSM1382284 Query DataSets for GSM1382284
Status Public on May 08, 2014
Title RNA-seq shCEBPb exp3, 3T3-L1 4h
Sample type SRA
 
Source name 3T3-L1 pre-adipocytes (4h)
Organism Mus musculus
Characteristics cell line: 3T3-L1
differentiation stage: pre-adipocytes
time: 4 hrs
treatment: Lentivirus expressing shRNA against C/EBPβ
Treatment protocol 3T3-L1 pre-adipocytes (day 0) were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Cells were harvested four hours after induction.
Growth protocol 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days post confluency (day 0), the cells were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS).
Extracted molecule total RNA
Extraction protocol Purified RNA was subjected to standard mRNA sample preparation for sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions.
Data processing Sequence reads were mapped to the mouse genome (mm9) using Bowtie (Langmead et al., 2009, Genome biology, 10(3):R25). Mapped reads in exons were counted using HOMER (Heinz et al., 2010, Mol Cell, 38(4):576-89) and differentially expressed genes (adjusted P<0.05) were identified using DESeq (Anders and Huber, 2010, Genome Biology, 11(10):R106). Bedgraph files were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were created using HOMER for visualization of DHS and cutcount profiles as well as expression data in the UCSC genome browser.
 
Submission date May 07, 2014
Last update date May 15, 2019
Contact name Susanne Mandrup
E-mail(s) s.mandrup@bmb.sdu.dk
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL18480
Series (1)
GSE57415 Molecular architecture of transcription factor hotspots in early adipogenesis
Relations
BioSample SAMN02767380
SRA SRX535280

Supplementary file Size Download File type/resource
GSM1382284_SM373_RNA_shCEBPb_4h_exp3.fq.ucsc.bedGraph.gz 46.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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