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Sample GSM7840315 Query DataSets for GSM7840315
Status Public on Jan 29, 2024
Title BB16_tumor_rep2
Sample type SRA
 
Source name tumor
Organism Mus musculus
Characteristics tissue: tumor
cell line: B16-F10
cell type: whole tumor
treatment: Engrafted tumor
Treatment protocol NA
Growth protocol Six commonly used murine cancer cells lines (B16-F10, Pan02, MC38, LL2, EO771.LMB, and CT26) were cultured in cell culture-treated flasks at 37 degrees celcius and 5% CO2. CT26 was cultured in RPMI 1640 + 10% FBS + 1% P/S. B16-F10, LL2, and Pan02 were cultured in DMEM + 10% FBS + 1% P/S. EO771.LMB was cultured in DMEM + 20% FBS + 1% P/S + 20mM HEPES. MC38 was cultured in DMEM + 10% FBS + 1% P/S + 1% HEPES + 1% non-essential amino acid supplement + 1% sodium pyruvate. All reagents from Gibco. 500000 cells were injected into the flank of mice and tumor growth was monitored.
Extracted molecule polyA RNA
Extraction protocol At endpoint, tumors were excised from the mice and a tumor fragment was used for RNA isolation. RNA isolation was performed using the Rneasy Mini Kit (Qiagen) according to manufacturer's instructions.
PolyA enriched RNA, unstranded cDNA library, NEBNext library synthesis
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description SM4415
Data processing Aligned to mm10 using STAR (V2.5.0c)
Raw counttable was generated using HOMER
Normalised gene expression (RPKM) was analysed by HOMER
Differential gene expression analysis was analysed by DEseq2
Assembly: mm10
Supplementary files format and content: normalized gene count table as txt file
 
Submission date Oct 13, 2023
Last update date Jan 29, 2024
Contact name Lars Grøntved
E-mail(s) larsgr@bmb.sdu.dk
Phone +45 24 60 14 06
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL24247
Series (1)
GSE245293 Comparison of syngeneic tumor models reveals different tumor microenvironments with distinct subsets of cancer-associated fibroblasts polarized by infiltrating T cells
Relations
BioSample SAMN37803728
SRA SRX22084352

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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