|
| Status |
Public on Jul 20, 2022 |
| Title |
BMAd-Pnpla2+/+ CR, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/SJL
Sex: male
tissue: Bone marrow adipose tissue
age: 24 weeks old
genotype: BMAd-Pnpla2+/+
treatment: Caloric restriction
|
| Treatment protocol |
30% Caloric restriction (CR). After acclimation to single-housing for 2 weeks, and control diet (D17110202; Research Diets) for a week, daily food intake was measured for another week. Mice were then fed a 30% caloric restriction diet (D19051601; Research Diets) daily at ~6 pm, prior to onset of the dark cycle.
|
| Growth protocol |
Mice were housed in a 12 h light/dark cycle in the Unit for Laboratory Animal Medicine at the University of Michigan, with free access to water. Mice were fed ad libitum or underwent caloric restriction, as indicated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Distal tibiae were collected and cut ends. Bone marrow plugs were flushed out and homoginized with RNAStat60 reagent. DNA-free™ Kit was used to remove DNA before submitting for QC and RNAseq.
RNA libraries were prepared for sequencing using P_Stranded Library&Seq (PE100).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
3673
|
| Data processing |
The quality of the raw reads data was checked using FastQC (v.0.11.9).
The filtered reads were aligned to reference genome (UCSC mm10) using STAR with default parameters.
All samples passed the post-alignment quality check (QualiMap (v.2.2.1).
The DEseq2 method was used for differential expression analysis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 09, 2021 |
| Last update date |
Jul 20, 2022 |
| Contact name |
Ziru Li |
| E-mail(s) |
liziru@umich.edu
|
| Phone |
734-647-7721
|
| Organization name |
University of Michigan
|
| Department |
Molecular & Integrative Department
|
| Lab |
Ormond MacDougald
|
| Street address |
2800 Plymouth Rd.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE183784 |
Bone marrow adipocyte (BMAd)-specific deletion of Pnpla2 reveals local roles for lipolysis to fuel cells of bone and the marrow niche |
|
| Relations |
| BioSample |
SAMN21368504 |
| SRA |
SRX12122013 |
