|
| Status |
Public on Dec 01, 2023 |
| Title |
PDAC_Cold_stroma_2 |
| 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 |
FFPE blocks containing human primary tumors were serially sectioned onto Superfrost Plus microscope slides and glass slides with PEN membrane (Leica, catalog 11505158). Sections on Superfrost Plus microscope slides were used for automated immunohistochemistry to identify tumor epithelium and other cell types. PEN membrane slides were air dried and stored at -80 °C until analysis. These slides were thawed at room temperature prior to use and deparaffinized in fresh xylene for 30 seconds twice, followed by rehydration in ethanol (30 seconds each in 100%, 100%, 95%, and 70% ethanol). Slides were then transferred to RNase-free water and stained with Mayer’s hematoxylin for 10 seconds. Slides were washed with RNase-free water and dehydrated by submerging them in 95% ethanol, 100% ethanol, and xylene, twice in each solution for 30 seconds. Specific regions of dehydrated slides were then microdissected by laser capture using a LMD7000 microscope (Leica). RNA from cold and hot tumor stroma and epithelium was collected using a NucleoSpin total RNA FFPE XS kit (Takara, catalog 740969.50).
Sequencing libraries were prepared using a SMARTer stranded total RNA-Seq kit v2 (Takara) 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) |
| GSE155724 |
Spatial coupling of microbes and immune cells in solid malignancies [LCM_cold_hot_tumor_nest] |
| GSE155725 |
Spatial coupling of microbes and immune cells in solid malignancies |
|
| Relations |
| BioSample |
SAMN15734741 |
| SRA |
SRX8889918 |
