|
| Status |
Public on Sep 01, 2022 |
| Title |
BMAd-DTA [FOD9088] |
| Sample type |
SRA |
| |
|
| Source name |
BMAd-DTA
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/SJL
tissue: Distal tibial bone; whole bone
age: 24 weeks old
genotype: BMAd-DTA
treatment: Ad libitum
|
| Treatment protocol |
No specific treatment was applied.
|
| 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 and food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Distal tibiae were collected by cutting through tibia/fibula junction. Whole distal tibial bones were snap-frozen, hammered into powder, 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 |
| |
|
| 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.
Assembly: UCSC mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 01, 2022 |
| Last update date |
Sep 01, 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) |
| GSE199973 |
Constitutive bone marrow adipocytes suppress local bone formation and support hematopoietic stem and progenitor cells |
|
| Relations |
| BioSample |
SAMN27181226 |
| SRA |
SRX14697584 |
