|
| Status |
Public on Sep 21, 2019 |
| Title |
GSC528-WT |
| Sample type |
SRA |
| |
|
| Source name |
GSCs_WT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GSC528
cell type: Patient-derived glioma stem-like cells (GSCs)
genotype/variation: wild-type
|
| Treatment protocol |
GSCs were infected with CRISPR/Cas9 lentivirus that targeting SRSF3 for KO or control. After 5-8 days, cells were harvested to extract RNA.
|
| Growth protocol |
Patient-derived GSCs that were cultured in DMEM/F12 medium (Thermo Fisher Scientific, 11320-033) containing 2% B27 supplement (Thermo Fisher Scientific, 17504-044), 1% penicillin and 1% streptomycin (Thermo Fisher Scientific, 11860-038), 5 μg/ml heparin (Sigma-Aldrich, 9041-08-1), 20 ng/ml EGF (Peprotech, 100-15R0, and 20 ng/ml bFGF (Peprotech, 100-18B).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNeasy Mini kit according to the manufacturer's instruction.
Libraries were prepared using the Illumina stranded Total RNA TruSEQ kit according to the manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the human genome hg19 using HISAT2 (Galaxy Version 2.1.0+galaxy4).
Quantification was performed using HTSeq-count (Galaxy Version 0.9.1).
Differential expression of genes was calculated by DESeq2 (Galaxy Version 2.11.40.2).
The mapped reads were processed through the MISO (version 0.5.4) pipeline to estimate expression of alternatively spliced isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: tabular files include raw counts for each transcript of each sample generated from HTSeq-count; txt files include Percent Spliced In (PSI) values for each AS events of each sample calculated by MISO.
|
| |
|
| Submission date |
Apr 30, 2019 |
| Last update date |
Sep 21, 2019 |
| Contact name |
Xiao Song |
| E-mail(s) |
xiao.song@northwestern.edu
|
| Phone |
3122738044
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Neurology
|
| Lab |
Shiyuan Cheng
|
| Street address |
303 E Superior St, Lurie 6-250
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE130501 |
Transcriptome-wide analysis of wild-type and SRSF3-knockout glioma stem-like cells |
|
| Relations |
| BioSample |
SAMN11538781 |
| SRA |
SRX5771115 |
