|
| Status |
Public on Jul 01, 2024 |
| Title |
G19.Scr.3 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GIC19
cell type: Glioblastoma initiating cells
genotype: WT
|
| Growth protocol |
GIC were maintained in NeuroCult NS-A Proliferation kit medium, 1% Pen/Strep, 2µg/ml Heparin, 20ng/ml murine EGF and 10ng/ml human FGF. iNSC were cultured in 0.5X Advanced DMEM/F-12 , 0.5X Neurobasal medium, 1X Neurobasal Induction supplement and 1X pen/strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction with NORGEN Biotek DNA/RNA/Protein Purification Plus kit. 1ug of total RNA used for library construction
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA. Illumina PE150 technology
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GIC19_log2RPKM_annot.csv
|
| Data processing |
Reads were quality trimmed using trimgalore v0.6.5
Counting of reads was performed with RSEM v1.3.1
Differential expression analysis was performed in DESeq2 using the Wald test
Gene set enrichment analysis was performed using R package fgsea and the ranked DESeq2 Wald statistic of all genes
Assembly: genome GRCh37 (hg19) using STAR v2.7.9a
Supplementary files format and content: comma separated values of log2RPKM of GIC samples
Supplementary files format and content: comma separated values of log2RPKM of NSC samples
|
| |
|
| Submission date |
Sep 05, 2023 |
| Last update date |
Jul 01, 2024 |
| Contact name |
James Nicholson |
| E-mail(s) |
[email protected]
|
| Organization name |
Queen Mary University of London
|
| Department |
Blizard Institute
|
| Street address |
4 Newark St
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE242328 |
METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma [RNAseq] |
| GSE243132 |
METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma |
|
| Relations |
| BioSample |
SAMN37283928 |
| SRA |
SRX21635751 |
