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Sample GSM8004874 Query DataSets for GSM8004874
Status Public on May 17, 2024
Title USP43 KO hypoxia biol rep 2
Sample type SRA
 
Source name HeLa
Organism Homo sapiens
Characteristics cell line: HeLa
genotype: USP43 KO
treatment: hypoxia
Treatment protocol Hypoxic cell culture was performed in a Whitley H35 Hypoxystation at 37 °C, 5% CO2, 1 % O2and 94% N2.
Growth protocol HeLa cells were maintained in DMEM and supplemented with 10% FCS
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from HeLa cells using the RNeasy Plus minikit.
RNA libraries for RNA-Seq were prepared by GeneWiz (NEBNext Ultra II RNA Library Prep Kit)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with TrimGalore
Transcript quantification was performed using Salmon
Differential transcript analysis was performed with DESeq2
Assembly: Gencode Human Release 44 (GRCh38.p14)
Supplementary files format and content: Salmon quant files that contain TPM values for each transcript
 
Submission date Jan 05, 2024
Last update date May 17, 2024
Contact name Niek Wit
E-mail(s) nw416@cam.ac.uk
Organization name University of Cambridge
Department Department of Medicine
Lab Professor James Nathan
Street address Puddicombe Way
City Cambridge
State/province Not US or Canada
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24676
Series (2)
GSE252654 Deubiquitinating enzyme mutagenesis screens identify a USP43 driven HIF-1 transcriptional response [RNA-seq]
GSE252655 Deubiquitinating enzyme mutagenesis screens identify a USP43 driven HIF-1 transcriptional response
Relations
BioSample SAMN39275521
SRA SRX23114729

Supplementary file Size Download File type/resource
GSM8004874_USP43-hypoxia-2_quant.sf.gz 3.0 Mb (ftp)(http) SF
SRA Run SelectorHelp
Raw data are available in SRA

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