|
| Status |
Public on Feb 06, 2018 |
| Title |
GSC-827-NSC-1 |
| Sample type |
SRA |
| |
|
| Source name |
GSC-0827_shControl
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GSC-0827
cell type: GBM stem-like cells (GSCs)
shRNA: shControl
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
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 |
GSC-0827 replicate 1
827-NSC-1
|
| Data processing |
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
All data was combined and normalized using a CPM method from the R/Bioconductor package, edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each Sample.
|
| |
|
| Submission date |
Feb 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
|
| Organization name |
FHCRC
|
| Street address |
1100 Fairview Ave N,
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE95027 |
ZNF131 suppresses centrosome fragmentation in Glioblastoma stem-like cells through regulation of HAUS5 |
|
| Relations |
| BioSample |
SAMN06345024 |
| SRA |
SRX2573639 |
