|
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 |