|
Status |
Public on Dec 01, 2023 |
Title |
75755T_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 |
SAMN15734722 |
SRA |
SRX8889906 |