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Sample GSM5536829 Query DataSets for GSM5536829
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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