|
| Status |
Public on Jan 29, 2024 |
| Title |
Pan01_tumor_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell line: Pan02
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 |
SM4420
|
| 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 |
SAMN37803723 |
| SRA |
SRX22084357 |
