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Sample GSM7713325 Query DataSets for GSM7713325
Status Public on Jun 26, 2024
Title 2283546_NEJF10-3D-Hyp-02
Sample type SRA
 
Source name NEJF10
Organism Mus musculus
Characteristics cell line: NEJF10
cell type: HB
treatment: 3D Culture with 1% O2
Treatment protocol NEJF10 cells were cultured in 21% and 1% oxygen in monolayer, or 21% oxygen in 3D spheroid.
Growth protocol NEJF10 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2 with 21% oxygen or 1% oxygen.
Extracted molecule total RNA
Extraction protocol Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60) and mapped to mouse reference gennome(STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (M22).
Assembly: GRCm38(mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files
 
Submission date Aug 16, 2023
Last update date Jun 26, 2024
Contact name Hongjian Jin
E-mail(s) hongjian.jin@STJUDE.ORG
Organization name St Jude Children's Research Hospital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38015
Country USA
 
Platform ID GPL24247
Series (1)
GSE240980 Cellular fitness of MYC-driven cancer cells to genetic and pharmacologic perturbations in normoxia, hypoxia and 3D
Relations
BioSample SAMN37006693
SRA SRX21382762

Supplementary file Size Download File type/resource
GSM7713325_2283546_NEJF10-3D-Hyp-02.RSEM.genes.results.gz 1.2 Mb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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