|
| Status |
Public on May 01, 2020 |
| Title |
PTU sample 11 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal primary tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissues were removed, flash frozen on dry ice, and RNA was harvested using the mini RNA extraction kit (Qiagen, Germany; 74106). Sequencing was performed by the GeneCore at the EMBL (Heidelberg, Germany) on an Illumina HiSeq 2000 platform using the Truseq stranded mRNA kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
19s002149
|
| Data processing |
Transcript level quantification was performed by using the Salmon Transcription Quantification package (version 0.9.1) on Galaxy server with default parameters.
Homo sapiens geonome assembly GRCh38 (hg38) was used as the reference genome.
Gene level quantification was performed by using R/Bioconductor package "tximport" with EnsDb.Hsapiens.v86 annotation package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values at gene level (Ensembl Gene ID)
|
| |
|
| Submission date |
Feb 18, 2020 |
| Last update date |
May 01, 2020 |
| Contact name |
Thomas Schmidt |
| E-mail(s) |
thomas.schmidt1@med.uni-heidelberg.de
|
| Organization name |
University Hospital Heidelberg
|
| Department |
Department of General, Visceral and Transplantation Surgery
|
| Street address |
Im Neuenheimer Feld 110
|
| City |
Heidelberg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE145429 |
Reducing metastases stiffness by targeting fibroblasts improves therapeutic outcome in colorectal cancer [Tissue] |
| GSE145432 |
Reducing metastases stiffness by targeting fibroblasts improves therapeutic outcome in colorectal cancer |
|
| Relations |
| BioSample |
SAMN14124259 |
| SRA |
SRX7737604 |
