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Sample GSM7089498 Query DataSets for GSM7089498
Status Public on Oct 06, 2024
Title Muscle vdr 7wk rep 2
Sample type SRA
 
Source name Muscle
Organism Mus musculus
Characteristics tissue: Muscle
genotype: vdr-/-
Treatment protocol Skeletal muscles from the hind limbs (QUAD) were dissected, transferred to 1 ml RNAIsoPlus (Takara) and flash frozen in liquid nitrogen.
Growth protocol WT (C57BL/6J) and VDR knockout (B6.129S4-Vdrtm1Mbd/J mice) were genotyped and weaned at 21 days and subjected to regular chow and water (ad libitum)
Extracted molecule total RNA
Extraction protocol The frozen tissue samples were ground in liquid nitrogen, added 1 ml of RNAIsoPlus and allowed to thaw. The samples were extracted for 10 minutes at room temperature followed by addition of 200μl chloroform. After vortexing, the samples were centrifuged at maximum speed for 5 minutes. The aqueous layer was transferred to fresh tubes and precipitated with isopropanol.
RNA libraries for RNA-seq were prepared using TruSeq RNAseq library prep kit v2 following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequence reads were trimmed for adaptor sequence/low-quality sequence trimmomatic
Trimmed sequence reads were mapped to GRCM38/mm10 and the reads per gene were counted using STAR.
Normalization and differential expression analysi swere performed using DEseq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample
 
Submission date Mar 09, 2023
Last update date Oct 06, 2024
Contact name G Aneeshkumar Arimbasseri
E-mail(s) aneesh@nii.ac.in
Phone +91 9971986746
Organization name National Institute of Immunology
Department Molecular Genetics Laboratory
Lab Molecular Genetics Laboratory
Street address Aruna Asaf Ali Marg
City New Delhi
State/province Delhi
ZIP/Postal code 110067
Country India
 
Platform ID GPL24247
Series (1)
GSE226988 Vitamin D signaling orchestrates skeletal muscle metabolic flexibility by modulating its fuel choice
Relations
BioSample SAMN33697595
SRA SRX19610465

Supplementary file Size Download File type/resource
GSM7089498_counts_V7ReadsPerGene.out.tab.gz 222.5 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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