|
| Status |
Public on Feb 15, 2023 |
| Title |
G523_ScrB [RNA-seq KD] |
| Sample type |
SRA |
| |
|
| Source name |
glioblastoma G523
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: Scr
|
| Treatment protocol |
2 ug/mL doxycycline x 7 days
|
| Growth protocol |
Grown in serum-free conditions on laminin-PLO coated plates with FGF and EGF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested using Accutase and PBS; RNA was extracted from 1 million cells using the RNEasy Mini Kit (Qiagen) as per manufacturer instructions. RNA was quantified using the Nanodrop.
Libraries were constructed at the Center for Health Genomics and Informatics using the NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) with ribosomal RNA depletion
Samples were sequenced on a NextSeq 500 for 150 cycles (single-end; 1x75bp)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were pseudoaligned to the human transcriptome (GRCh38.rel79) using kallisto, and differential analysis was performed using sleuth
Genome_build: hg38
|
| |
|
| Submission date |
Apr 24, 2020 |
| Last update date |
Feb 15, 2023 |
| Contact name |
Marco Gallo |
| Organization name |
University of Calgary
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Gallo lab
|
| Street address |
2500 University Dr NW
|
| City |
Calgary |
| State/province |
AB |
| ZIP/Postal code |
T2N 1N4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE149324 |
MacroH2A2 knockdown vs control RNA-seq in primary glioblastoma cells |
|
| Relations |
| BioSample |
SAMN14691770 |
| SRA |
SRX8173513 |
