|
| Status |
Public on Jul 03, 2015 |
| Title |
Setdb1_Δ/Δ_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: IL-7 Cultured pro-B cell
setdb1: Δ/Δ
bcl2: bcl2-tg
|
| Growth protocol |
Murine bone marrow-derived pro-B cells were isolated and purified by FACS. Cells were then clutured for four days in media containing 5 ng/µl of IL-7 (Invitrogen, PMC0075).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified from day four cultures using QIAGEN Rneasy kits, followed by ribodepletion (Ribo-Zero, Epicentre).
Libraries were prepared using TruSeq RNA Sample kits with indexed adaptors (Illumina). Libraries pooled from two samples were subjected to 101 bp paired-end sequencing using an Illumina HiSeq2000 (San Diego CA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-Seq data were aligned to the transcriptome and reference genome (mm10) using TopHat 2.0.9
RPKM values of ERV families was obtained using RSeQC
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedTools; Scores represent total reads
|
| |
|
| Submission date |
Jun 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Collins |
| E-mail(s) |
patlennycollins@yahoo.com
|
| Organization name |
Washington University
|
| Department |
Pathology and Immunology
|
| Lab |
Oltz
|
| Street address |
1217 Oakleaf dr
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63119 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE69464 |
SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes [RNA-Seq] |
| GSE69504 |
SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes |
|
| Relations |
| BioSample |
SAMN03758674 |
| SRA |
SRX1047270 |
