|
| Status |
Public on Aug 25, 2023 |
| Title |
U2OS cells, siNT_HU_VE_R1 |
| Sample type |
SRA |
| |
|
| Source name |
siNT_HU_VE
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
sirna transfection: Non-targeting control siRNA
treatment: HU + 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_HV1
|
| 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 |
SAMN20972480 |
| SRA |
SRX11908920 |
