NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7157131 Query DataSets for GSM7157131
Status Public on May 17, 2024
Title Control, TAMs, mouse 954
Sample type SRA
 
Source name Sub-cutaneous tumor
Organism Mus musculus
Characteristics tissue: Sub-cutaneous tumor
cell line: B6CaP
cell type: Tumor associated macrophages
genotype: Male C57BL/6J
treatment: PBS oral gavage
Treatment protocol Each mouse was treated with either PBS (control) or JHU083 by oral gavage.
Growth protocol B6CaP cells were injected subcutaneously into the flank region of each mouse.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from sorted tumor associated macrophages (Live CD45+CD3-Ly6G-CD11b+F4/80+) with Trizol (Thermofisher) based on manufacturer's protocol.
RNA was converted to cDNA with the Ovation RNA-seq System v2.0 kit and library construction was performed with the Truseq Nano kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing rsem-1.3.0 was used for alignment to the mm39 genome and for the generation of gene expression levels.
The following options were used in the rsem-calculate-expression module: --star --calc-ci --star-output-genome-bam --forward-prob 0.5
Differential expression analysis and statistical testing was performed with DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files from the rsem pipeline, including counts, TPM, and FPKM for each sample
Supplementary files format and content: DESeq2 results comparing JHU083-treated TAMs versus control TAMs
 
Submission date Apr 07, 2023
Last update date May 17, 2024
Contact name Alex Jea-Eun Lee
E-mail(s) alee262@jhmi.edu
Organization name Johns Hopkins University
Street address 1650 Orleans Street
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platform ID GPL24247
Series (2)
GSE229222 Glutamine antagonist JHU083 reprograms immunosuppressive tumor-associated macrophages to drive tumor immunity in urologic cancers, bulk RNA-seq
GSE230162 Glutamine antagonist JHU083 reprograms immunosuppressive tumor-associated macrophages to drive tumor immunity in urologic cancer
Relations
SRA SRX19907614
BioSample SAMN34116266

Supplementary file Size Download File type/resource
GSM7157131_Monali_954_rsem_mm39.genes.results.gz 1.3 Mb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap