|
| Status |
Public on Jun 18, 2014 |
| Title |
RNA-seq normal pre-B 1 |
| Sample type |
SRA |
| |
|
| Source name |
pre-B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pre-B cells
immunophenotype: GFP+B220+IgM–Kit–CD25+
treatment: 3 days Dox (induction of control shRNA)
cell source: bone marrow of CAG-rtTA3;TRE-GFP-shLuc.1309 bitransgenic mouse
|
| Treatment protocol |
Mice were treated with Dox for 3 days, resulting in the expression of a GFP-linked control shRNA that is assumed to have minimal impact on global gene expression
|
| Growth protocol |
Bone marrow cells were isolated from mice and pre-B cells were isolated using FACS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorted cell pellets were lysed and RNA prepared using QIAGEN RNEasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Illumina CASAVA version 1.8.2
A069
|
| Data processing |
Illumina CASAVA pipeline used for basecalling
RNA-seq reads were aligned to the mouse genome by Rsubread version 1.7.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm9 (NCBI build 37.2)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene
|
| |
|
| Submission date |
Dec 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
[email protected]
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE52868 |
Expression profiling of mouse bone marrow pre-B cells |
|
| Relations |
| BioSample |
SAMN02428732 |
| SRA |
SRX385647 |
