|
Status |
Public on Jan 25, 2017 |
Title |
GSC4_RNAseq_rep2 |
Sample type |
SRA |
|
|
Source name |
GSC4
|
Organism |
Homo sapiens |
Characteristics |
cell line: Patient-derived neurosphere line GSC4 drug treatment: none
|
Treatment protocol |
Cells were treated with drugs with a final DMSO concentration of either 0.1 or 0.15% DMSO.
|
Growth protocol |
Neurosphere cultures were maintained in Neurobasal media supplemented with 20 ng/mL recombinant EGF (R and D Systems), 20ng/mL FGF2 (R and D Systems), 1X B27 supplement (Invitrogen), 0.5X N2 supplement (Invitrogen), 3mM L-glutamine, and penicillin/ streptomycin.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Whole RNA was extracted from 1-3×10e6 cells using the QIAGEN RNeasy kit according to the manufacturer’s protocol. For RNA-seq library preparation, Poly(A)+ RNA was enriched using magnetic oligo(dT)-beads (Life Technologies) and fragmented to 200–600 base pairs and then ligated to RNA adaptors using T4 RNA Ligase (NEB).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Paired-end reads were aligned to UCSC transcriptome (hg19) using Bowtie (version 0.12.7) with the following parameters: --chunkmbs 512 -q --phred33-quals -n 0 -l 25 -I 1 -X 2000 -p 6 -a -m 15. Gene expression, quantified as transcript per million (TPM), was estimated using RSEM with the following parameters: --fragment-length-max 1000 --estimate-rspd --paired-end. Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
|
|
Submission date |
Oct 14, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Cem Sievers |
E-mail(s) |
csievers@mgh.harvard.edu
|
Organization name |
MGH
|
Department |
Molecular Pathology
|
Lab |
Bernstein
|
Street address |
165 Cambridge Street
|
City |
Boston |
ZIP/Postal code |
02114 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE74557 |
Adaptive chromatin remodeling in glioblastoma stem cell plasticity and drug tolerance |
|
Relations |
BioSample |
SAMN05908315 |
SRA |
SRX2245384 |