|
| Status |
Public on Mar 17, 2023 |
| Title |
U87 NFKB2 KD TWEAK rep 3 [U87_RNAseq_NFKB2KD_TW3] |
| Sample type |
SRA |
| |
|
| Source name |
U-87MG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U-87MG
genotype: NFKB2 KD
treatment: TWEAK
|
| Growth protocol |
U-87MG cells were seeded in DMEM + 10% FBS. After 24h, cells were starved in optimem for 8h then treated with 10ng/ml TWEAK for 48h. TWEAK was replenished after 24h.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Trizol and treated with Dnase.
RNA-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol through the polyA mRNA workflow
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using STAR
featureCounts was used to extract raw counts
Differential analysis was performed with DESeq2
Assembly: hg38
Supplementary files format and content: bigwig (files for each ChIP provided were merged from two biological replicates), narrowPeak
|
| |
|
| Submission date |
Feb 26, 2023 |
| Last update date |
Mar 17, 2023 |
| Contact name |
Yinghui Li |
| E-mail(s) |
liyh@ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
05n-21
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE207982 |
NF-κB/p52 augments ETS1 binding genome-wide to promote glioma progression |
|
| Relations |
| BioSample |
SAMN33450606 |
| SRA |
SRX19507878 |
