|
| Status |
Public on Oct 08, 2020 |
| Title |
Input2 |
| Sample type |
SRA |
| |
|
| Source name |
human cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GSC11
cell type: Glioblastoma stem cell line
antibody: NA
|
| Growth protocol |
GSC11 cells were cultured as tumorspheres in DMEM/F12 medium supplemented with B27 supplement (Life Technologies), bFGF and EGF (20 ng/mL each). Cells were grown in a 5% CO2 cell culture incubator at 37℃.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was isolated from GSC11 cells using Trizol reagent (Thermo Fisher). Poly (A) mRNA was subsequently purified from total RNA using GenElute™ mRNA Miniprep Kit (Sigma). For IP samples, mRNA was sonicated and subjected to IP using YTHDF2 antibody (Proteintech #24744-1-AP).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
All samples were sequenced by Illumina HiSeq 2500 with single-end 50-bp read length. The deep sequencing data were mapped to human genome version 37 (GRCh37).
After reads were mapped with hisat2, Stringtie was used to calculate the read counts of each gene which represent their transcriptional expression level. Then we performed DEseq2 to calculate normalized reads counts in each gene and detect enriched transcripts with a double threshold on the log2-fold change (>1) and the correspondent statistical significance (P-value < 0.05).
Genome_build: GRCh37
Supplementary_files_format_and_content: excel file containing log2-fold change between input and IP samples
|
| |
|
| Submission date |
Jan 02, 2020 |
| Last update date |
Oct 08, 2020 |
| Contact name |
Youqiong Ye |
| E-mail(s) |
youqye@gmail.com
|
| Phone |
+8613661565591
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
280 Chongqing south road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE142827 |
EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma [RIP-Seq] |
| GSE142828 |
EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma |
|
| Relations |
| BioSample |
SAMN13708198 |
| SRA |
SRX7488391 |
