|
| Status |
Public on Apr 13, 2016 |
| Title |
OSMR-KD1_EGFRvIII expressing astrocytes |
| Sample type |
SRA |
| |
|
| Source name |
Astrocyte cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Astrocyte
derivation: EGFRvIII-expressing astrocytes were established as previously described (de La Iglesia et al 2008, Genes and Dev, 22(4):449-62.).
genotype/variation: OSMR-KD1_EGFRvIII expressing
|
| Treatment protocol |
No specific tratment was carried out on any of the cells prior to harvesting them for ChIP-Seq or RNA-Seq studies.
|
| Growth protocol |
Glial cells were grown in DMEM media supplied with 10% FBS. Brain tumor Stem cells were grown in BTSC media according to manufacturer instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy kit (Qiagen).
The quality of RNA was assessed by bioanalyzer prior to sequencing. Libraries were prepared according to Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
shOSMR1 was introduced into astrocytes by lentiviral mediated delivery and selection with blasticidin
Sample 1
|
| Data processing |
Reads processed with CASAVA v1.8.2 to generate fastq
Reads mapped with tophat (v.1.4.1) guided by transcripts from Ensembl release 67
Transcripts annotated with cufflinks (v.1.3.0)
Genome build: mm9
Supplementary files format and content: Tab-delimited .txt file containing gene symbols, gene locations and FPKM expression values
|
| |
|
| Submission date |
Sep 30, 2013 |
| Last update date |
May 15, 2019 |
| Organization |
Ottawa Hospital Research Institute |
| Phone |
(613) 737-8899 -73255
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Ottawa Bioinformatics Core Facility
|
| Street address |
501 Smyth Rd.
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE51281 |
EGFRvIII/STAT3 targets in glioblastoma pathogenesis |
|
| Relations |
| BioSample |
SAMN02369905 |
| SRA |
SRX361665 |
