|
| Status |
Public on Aug 29, 2022 |
| Title |
Female aged Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
bone endothelial cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: freshly isolated from tibia
cell type: bone endothelial cells
age: 65 weeks
Sex: F
strain: c57/Bl6
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bone endothelial cells were purified using endomucin expression and sorted directly into lysis buffer of the RNeasy Plus Micro Kit (QIAGEN). Total RNA was isolated as per the manufacturer’s guidelines.
RNA quality was checked using a 2100 BioAnalyzer (Agilent), and libraries were prepared with TruSeq Total RNA Library Preparation Kit (Illumina) following the manufacturer’s guidelines. Sequencing of libraries was carried out at the LMS Genomics Facility on an Illumina HiSeq 2500 platform with 100-nucleotide-length paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
F.65weeks.3
|
| Data processing |
The reads were aligned to mouse genome mm9 using Tophat2 with arguments “-r 100 -N 2 --b2-very-sensitive --library-type fr-firststrand --b2-L 25” with gene annotation from Ensembl version 67
Gene-based read count was obtained using htseq-count function from HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample
|
| |
|
| Submission date |
Dec 18, 2020 |
| Last update date |
Aug 29, 2022 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE163515 |
Gene expression analysis of male and female bone endothelial cells from 2 and 65 weeks old mice |
|
| Relations |
| BioSample |
SAMN17116131 |
| SRA |
SRX9703859 |
