|
Status |
Public on Nov 10, 2023 |
Title |
anti-CD40_1 |
Sample type |
SRA |
|
|
Source name |
Tumor
|
Organism |
Mus musculus |
Characteristics |
tissue: Tumor cell line: PDA.7940B cell type: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma genotype: WT treatment: anti-CD40 (FGK45, 0.1mg IP x1)
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 5μm serial sections obtained from FFPE tissues using the RNeasy FFPE kit (Qiagen). 3’ mRNA-seq libraries were generated from 100ng of DNAseI treated total RNA using the QuantSeq FWD Library Preparation kit (Lexogen), according to manufacturer’s directions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
CD40a1 allsamples.deseq.normalized.counts.csv
|
Data processing |
FASTQ files were uploaded to the BaseSpace Suite (Illumina) and aligned using its RNA-Seq Alignment application (version 2.0.2), in which STAR was selected to align sequences with maximum mismatches set to 14 as recommended by Lexogen. Differentially expressed genes were determined using the DESeq2 package. Assembly: mm10 Supplementary files format and content: *.csv file with DESeq2 normalized counts of all samples
|
|
|
Submission date |
May 18, 2023 |
Last update date |
Nov 10, 2023 |
Contact name |
Max M Wattenberg |
E-mail(s) |
max.wattenberg@pennmedicine.upenn.edu
|
Organization name |
University of Pennsylvania
|
Lab |
Beatty
|
Street address |
3400 Civic Center Blvd
|
City |
Philadelphia |
State/province |
PENNSYLVANIA |
ZIP/Postal code |
19104 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE232860 |
Cancer immunotherapy via synergistic co-activation of myeloid cells [RNA-seq] |
GSE233175 |
Cancer immunotherapy via synergistic co-activation of myeloid cells |
|
Relations |
BioSample |
SAMN35167360 |
SRA |
SRX20432828 |