|
Status |
Public on Aug 25, 2023 |
Title |
U2OS cells, siNT_VE_R1 |
Sample type |
SRA |
|
|
Source name |
siNT_VE
|
Organism |
Homo sapiens |
Characteristics |
cell line: U2OS sirna transfection: Non-targeting control siRNA treatment: VE-822
|
Treatment protocol |
U2OS cells were treated with 2 mM of hydroxyurea (HU), or 2 µM VE-822 (VE), or with 2 mM HU and 2 µM VE for 4 hours, and siNT or siSETD2
|
Growth protocol |
U2OS cells were grown in Dulbecco's modified Eagle medium (GIBCO) with 10% fetal bovine serum (FBS) supplemented with penicillin and streptomycin (Invitrogen).
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was purified from cell pellets with the RNeasy mini kit (Qiagen) Libraries were prepared according to the protocols of NEBNext® UltraTM RNA Library Prep Kit for Illumina
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
NT_V1
|
Data processing |
Data QC using FastQC, and reads trimmed 22 from the left and 22 from the right (Illumina Adaptors) Mapping to the hg38 genome was performed with STAR v2.6.1d (Parameter: mismatch = 2) Quantification was performed with FeatureCounts v1.5.0-p3 Differential Analysis was performed using DESeq2 v1.26.0 (padj<=0.05) Genome_build: hg38 Supplementary_files_format_and_content: fpkm matrix table for each condition
|
|
|
Submission date |
Aug 25, 2021 |
Last update date |
Aug 25, 2023 |
Contact name |
Linda van Bijsterveldt |
E-mail(s) |
linda.vanbijsterveldt@lmh.ox.ac.uk
|
Organization name |
Oxford Institute for Radiation Oncology
|
Lab |
Tim Humphrey's Lab
|
Street address |
Old Road Campus
|
City |
Oxford |
State/province |
non-US Resident |
ZIP/Postal code |
OX3 7DQ |
Country |
United Kingdom |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE182775 |
Histone H3K36me3 regulates E2F transcription as part of the DNA replication stress checkpoint response |
|
Relations |
BioSample |
SAMN20972477 |
SRA |
SRX11908918 |