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Sample GSM4711243 Query DataSets for GSM4711243
Status Public on Dec 01, 2023
Title 76863T_PDAC
Sample type SRA
 
Source name RNA isolated from FFPE block
Organism Homo sapiens
Characteristics diagnosis: Pancreatic ductal adenocarcinoma
tissue: Pancreas
Extracted molecule total RNA
Extraction protocol For isolation of RNA from whole slides, FFPE sections on Superfrost Plus microscope slides were collected via mechanical scrapping, and RNA was isolated using a RNeasy FFPE kit (Qiagen, catalog 73504) following the manufacturer’s protocol.
Sequencing libraries were prepared using a QuantSeq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen) following manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing FASTQ files uploaded to the BaseSpace Suite (Illumina) were aligned using its RNA-Seq Alignment application (version 2.0.0).
Output files were then analyzed using RNA-Seq Differential Expression application (version 1.0.1) in the BaseSpace suite.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file contains TPM values of all samples.
 
Submission date Aug 05, 2020
Last update date Dec 01, 2023
Contact name Gregory L. Beatty
E-mail(s) gregory.beatty@pennmedicine.upenn.edu
Phone (215) 746-7764
Organization name University of Pennsylvania
Department Medicine
Street address 3400 Civic Center Blvd, South Pavilion, Rm 8-107
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL18573
Series (2)
GSE155722 Spatial coupling of microbes and immune cells in solid malignancies [Whole_slides]
GSE155725 Spatial coupling of microbes and immune cells in solid malignancies
Relations
BioSample SAMN15734719
SRA SRX8889909

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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