|
| Status |
Public on Dec 01, 2023 |
| Title |
70204T_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 |
SAMN15734725 |
| SRA |
SRX8889903 |
