|
| Status |
Public on Jan 01, 2024 |
| Title |
Tumor necrotic core, Rat3875 |
| Sample type |
SRA |
| |
|
| Source name |
mammary tumor
|
| Organisms |
Mus musculus; Rattus norvegicus |
| Characteristics |
tissue: mammary tumor
cell line: 4T1
cell type: breast cancer
genotype: wildtype
treatment: no treatment
|
| Growth protocol |
4T1 cells transplanted into SRG host mammary fat pads and tissue collected after 27 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.
Library was constructed by Genewiz-Azenta using PolyA selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-seq of 4T1 xenograft tumor in rats: tumor necrotic core
|
| Data processing |
Reads trimmed with TrimGalore
Trimmed reads aligned to catenated mouse-rat genome using STAR.
Aligned reads mapped to genomic features using FeatureCounts
TMM library normalization and differential expression analysis performed with limma/voom pipeline
Assembly: GRCm38, Rnor_6.0
Supplementary files format and content: Processed data files “cpm_voom_tidy_mm.csv” and “cpm_voom_tidy_rn.csv” are files with a matrix of normalized gene-wise abundance values (CPM) for expression of rat(rn) or mouse (mm) genes. Tumor region column: in, out, lung corresponds to necrotic region (in), non-necrotic rim (out), or lung (lung).
Supplementary files format and content: Processed files ‘crossmap_gene_counts_mm.csv’ and “crossmap_gene_counts_rn.csv’ are unnormalized read counts mapped to the mouse (mm) or rat (rn) genomes using the disambiguation procedure. Columns correspond to samples
|
| |
|
| Submission date |
Jan 21, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Kevin J Cheung |
| E-mail(s) |
kcheung@fredhutch.org
|
| Organization name |
Fred Hutchinson Cancer Center
|
| Department |
Public Health Sciences
|
| Lab |
Chueng Lab
|
| Street address |
1100 Fairview Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL33050 |
| Series (1) |
| GSE223419 |
RNA sequencing of necrotic core and non-necrotic rim of tumors from 4T1 cell xenografts into rat |
|
| Relations |
| BioSample |
SAMN32815258 |
| SRA |
SRX19107757 |
