|
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
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|
|
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 |