|
Status |
Public on Nov 27, 2018 |
Title |
Gene expression from laser capture microdissected pancreatic cancer epithelium and stroma |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
|
Summary |
This study used laser capture microdissection to obtain paired tumor epithelium and stroma RNA samples from human pancreatic ductal adenocarcinoma (PDA) frozen sections. Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to model compartment-specific gene expression density on a genome-wide scale and build an algorithm for transcriptional devonvolution (ADVOCATE). RNA sequencing of macrodissected bulk PDA sections was performed on 15 samples in order to systematically compare TruSeq and NuGEN RNA-Seq libraries and (ii) correlate histopathological and molecular assessment of tumor composition.
|
|
|
Overall design |
Gene expression data are presented for 65 pairs of tumor epithelium and stroma LCM samples and 15 bulk tumors using NuGEN and TruSeq library preparation, respectively. Gene expression data are presented for 57 additional tumor stromas.
|
|
|
Contributor(s) |
Maurer HC, Olive KP |
Citation(s) |
30658994, 29249692, 29440233 |
|
Submission date |
Jan 09, 2017 |
Last update date |
Feb 02, 2021 |
Contact name |
Hans Carlo Maurer |
Organization name |
Klinikum rechts der Isar
|
Department |
II. Medizinische Klinik
|
Street address |
Ismaninger Str. 22
|
City |
Munich |
State/province |
Bavaria |
ZIP/Postal code |
81675 |
Country |
Germany |
|
|
Platforms (2) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
Samples (204)
|
|
Relations |
BioProject |
PRJNA360619 |
SRA |
SRP096338 |