|
| Status |
Public on Jan 29, 2021 |
| Title |
SOX10 OE repeat 1 dox |
| Sample type |
SRA |
| |
|
| Source name |
SOX10 over expression G144 cells passage 34
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Patient-derived Glioma stem cell line (G144)
host strain: NA
cell line: Patient derived line G144 expressing luciferase-GFP
patient derived xenograft: NA
facs sorting of tumour cells: NA
culture conditions: In vitro cell were cultured in defined media containing 10ng/ml of EGF and 10ng/ml of FGF
treatment: In vitro cells were exposed to 3mg/ml Doxycyline or untreated for 2 days prior to RNA extraction
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the RNAeasy Plus Mini Kit (Qiagen)
For RNA-seq of in vitro GSCs, oligo dT-based mRNA isolation was performed using the NEBNext Poly(A) mRNA magnetic isolation module. dsDNA libraries were prepared using NEB Ultra II directional RNA library prep kit and indexed using NEBNext® Multiplex Oligos.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Brooks_InVitro_RAW.csv
G144_p34_Dox
|
| Data processing |
Raw reads were aligned and feature counts extracted using the STAR aligner.
reference genome build:hg38
Supplementary_files_format_and_content: csv files containing unfiltered raw counts drom the STAR aligner
|
| |
|
| Submission date |
Oct 22, 2019 |
| Last update date |
Jan 29, 2021 |
| Contact name |
Sanjay Padmakar Khadayate |
| Organization name |
MRC London Institute of Medical Sciences
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE139261 |
RNA-seq analysis of in vivo region-specific PDX (G144) tumour cell populations and in vitro SOX10 overexpression in G144 cells |
|
| Relations |
| BioSample |
SAMN13087442 |
| SRA |
SRX7036336 |
