|
| Status |
Public on Oct 08, 2020 |
| Title |
siYTHDF2-2 |
| Sample type |
SRA |
| |
|
| Source name |
human cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GSC11
cell type: Glioblastoma-derived stem cells
transfection: YTHDF2 siRNA-2
|
| Treatment protocol |
GSC11 cells were transfected with control or YTHDF2 siRNAs (siControl-1, siControl-2, siYTHDF2-1, and siYTHDF2-2)
|
| 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 |
total RNA |
| Extraction protocol |
Total RNA was isolated from YTHDF2 knockdown (siYTHDF2) or control (siControl) GSC11 cells using Trizol reagent (Thermo Fisher).
The RNA-Seq library was generated using TruSeq Stranded mRNA Library Prep Kit (illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
transfected with YTHDF2 siRNA-2
|
| Data processing |
All samples were sequenced by NovaSeq 6000 sequencer with single end 100 bp read length. The deep sequencing data were mapped to human genome version 38(GRCh38.87).
After reads were mapped with HISAT2 version 2.1.0, StringTie v2.1.1 was used to calculate the read counts of each gene which represent their transcriptional expression level. Then we performed DEseq2 v1.26.0 to calculate normalized reads counts in each gene and detect enriched transcripts with a double threshold on the fold change (>1.5) and the correspondent statistical significance (P-adjust < 0.05).
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file containing read count and processed Fold change (siYTHDF2 vs siControl) for each gene
|
| |
|
| Submission date |
Aug 28, 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 |
GPL24676 |
| Series (2) |
| GSE142825 |
EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma [RNA-Seq] |
| GSE142828 |
EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma |
|
| Relations |
| BioSample |
SAMN15930128 |
| SRA |
SRX9028907 |
