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Sample GSM6948153 Query DataSets for GSM6948153
Status Public on Jan 01, 2024
Title Tumor non-necrotic rim, Rat3867
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 rim
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
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
BioSample SAMN32815262
SRA SRX19107745

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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