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Sample GSM4026009 Query DataSets for GSM4026009
Status Public on Jan 01, 2020
Title WT_Day0_2
Sample type SRA
 
Source name 3T3-L1
Organism Mus musculus
Characteristics cell type: 3T3-L1
differentiation stage: Start of differentiation
genotype/variation: wild type
Treatment protocol To start differentiation the cells were cultured until they reached complete confluence, and were then further incubated for another 48 h. After 48 h at 100 % confluence the medium was exchanged with differentiation medium, (DMEM with 10% FBS, 1 µM Dexamethasone, 0.5 mM IBMX and 1 µg/mL Insulin). The time point when differentiation medium was added is defined as the start of differentiation in our time course experiments (Day 0). After two days the differentiation medium was replaced by DMEM/ 10 % FBS containing insulin (1 µg/mL). At day 4 after start of differentiation the medium was exchanged with DMEM with 10 % FBS. At day 6 after start of differentiation the cells were harvested.
Growth protocol 3T3-L1 pre-adipocytes were purchased from American Type Culture Collection (ATCC). 3T3-L1 cells were cultured at 37°C in DMEM (Thermo-Fisher) containing 10 % calf serum (CS) (Sigma-Aldrich) in 5% CO2. The cells were cultured in 10 cm tissue culture dishes (TPP) and the medium was exchanged at least every 2 days. The pre-adipocytes never reached densities above 70% confluence unless they were subjected to differentiation.
Extracted molecule total RNA
Extraction protocol The RNA of cell extracts of an adipocyte time course experiment was purified using RNeasy Mini Kit (Quiagen).
TruSeq RNA stranded protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus, Ensembl GRCm38.p5, Release_91-2018-02-26
Supplementary_files_format_and_content: tab-delimited, raw counts
 
Submission date Aug 10, 2019
Last update date Jan 02, 2020
Contact name giancarlo russo
E-mail(s) giancarlo.russo@fgcz.ethz.ch
Organization name ETH/University of Zurich
Department Functional Genomics Center Zurich
Street address winterthurerstrasse 190
City Zurich
State/province Schweiz
ZIP/Postal code 8057
Country Switzerland
 
Platform ID GPL24247
Series (1)
GSE135683 Transcriptome analysis of adipocyte differentiation (3T3-L1 WT and MIGA2 perturbed/overexpressed)
Relations
BioSample SAMN12548842
SRA SRX6693261

Supplementary file Size Download File type/resource
GSM4026009_WT_Day0_2.txt.gz 119.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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