|
| Status |
Public on May 17, 2024 |
| Title |
JHU083, TAMs, mouse 957 |
| 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: JHU083 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 |
SRX19907620 |
| BioSample |
SAMN34116260 |
