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Sample GSM4685056 Query DataSets for GSM4685056
Status Public on Jul 23, 2021
Title SD_het3
Sample type SRA
 
Source name WAT
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Mof heterozygous
diet: standart diet
Treatment protocol Animals was kept in standart diet (SD) or high fat diet (HFD)
Growth protocol Tissue was extract directly from the animals
Extracted molecule polyA RNA
Extraction protocol  WAT was weighed and an equal amount of tissue was used to extract mRNA from  WAT. For RNA extraction from various sources were lysed directly in TRIZOL and samples were homogenized using an electric tissue homogenizer. Then, samples were incubated with 95% EtOH and transferred into mini-kit RNA extraction Zymo kit (R1054) and pure total RNA was extracted according to the manufacturer’s instructions. RNA concentrations were quantified on a Qubit 2.0 Fluorometer (Life Technology) and quality for deep sequencing checked by Fragment analyzer.
After quality control was then used to generate libraries using Illumina TruSeq RNA Sample Prep v2 (RS-122-2001). The manufacturer’s recommendations were followed and the libraries were sequenced on an Illumina NovaSeq6000 sequencer. All sequence data were performed in 3 biological replicates for SD group and duplicates for HFD group. The reads were conducted at 2 x 100 bp length.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads for mouse bulk RNA-seq datasets were mapped with following the default SnakePipes parameters of  bulk RNAseq pipeline (Bhardwaj et al. 2019). In brief, STAR software alignment against mouse genome version GRCm38. The total number of sequenced reads averaged 15 million pairs of which mean alignment of 65 % of the reads were uniquely mapped. Reads were counted with featureCounts (subread-1.5.0-p1). Differential expression analysis was performed with DESEQ2 (v1.26). Multi-FASTA QC statistics indicated data were of high quality and sequencing depth was sufficient to test for differential expression between conditions. Differential genes were called with an FDR threshold of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts
 
Submission date Jul 23, 2020
Last update date Jul 23, 2021
Contact name Asifa Akhtar
E-mail(s) akhtarlab_data@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Chromatin Regulation
Lab Akhtar Lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL24247
Series (2)
GSE154967 MOF haploinsufficiency triggers diet-induced obesity resistance (RNA-seq)
GSE156463 MOF haploinsufficiency triggers diet-induced obesity resistance
Relations
BioSample SAMN15618169
SRA SRX8806136

Supplementary file Size Download File type/resource
GSM4685056_SD_het3.tabular.txt.gz 180.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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