|
| Status |
Public on May 12, 2016 |
| Title |
RNA-Seq_MGG4_KD [Sample 4] |
| Sample type |
SRA |
| |
|
| Source name |
MGH4 Glioma stem-like cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MGG4
cell type: Glioma cell line
cell subtype: Cancer stem-like cells
infected with: shRNA sequence targeting Imp2
genotype/variation: IMP2 knockdown
|
| Treatment protocol |
MGH4 cell line infected with shRNA sequence targeting Imp2
|
| Growth protocol |
Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems). Puromycin selection for 5 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA extraction kit Exiqon, on colum DNASE treatment (Qiagen)
Illumina polyA stranded
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data: RNA_IMP2s_KD.txt
|
| Data processing |
Genomic alignment with TopHat 2.0.12, --b2-very-sensitive --library-type fr-firststrand --b2-N 1
Differential expression calling with edgeR 3.10.2 and R 3.2.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited textfile containing the raw readcounts, normalized cpm and gene fold-changes
|
| |
|
| Submission date |
Oct 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tommy Beat Schlumpf |
| Organization name |
ETH Zürich
|
| Department |
D-BSSE
|
| Lab |
Paro
|
| Street address |
Mattenstrasse 26
|
| City |
Basel |
| State/province |
Basel-Stadt |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE73845 |
Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [HTS] |
| GSE73847 |
Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines |
|
| Relations |
| BioSample |
SAMN04156651 |
| SRA |
SRX1317318 |
