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Sample GSM7384949 Query DataSets for GSM7384949
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

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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