|
| Status |
Public on May 08, 2024 |
| Title |
KFO-13 |
| Sample type |
SRA |
| |
|
| Source name |
primary pancreatic ductal adenocarcinoma (PDAC)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary pancreatic ductal adenocarcinoma (PDAC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ReliaPrep™ FFPE Total RNA Miniprep System (Promega)
TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat (Cat. N°20020596)
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 107
Assembly: hg38 gene version 107
Supplementary files format and content: Tab-delimited gene counts
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
May 08, 2024 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE228844 |
New strategies for the identification of intronic variants related to splicing events in pancreas cancer [RNA-Seq] |
| GSE229007 |
New strategies for the identification of intronic variants related to splicing events in pancreas cancer |
|
| Relations |
| BioSample |
SAMN34060269 |
| SRA |
SRX19857863 |
