|
| Status |
Public on Jan 25, 2017 |
| Title |
GSC8Per_RNAseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GSC8Per
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Patient-derived neurosphere line GSC8
drug treatment: chronic 1 µM dasatinib
|
| 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: BigWig density files
Supplementary_files_format_and_content: .tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Oct 12, 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 |
SAMN05898689 |
| SRA |
SRX2240102 |
