Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA360619

PRJNA360619: Gene expression from laser capture microdissected pancreatic cancer epithelium and stroma

Source: NCBI / GSE93326
Submission Date: Jan 09 2017
Release Date: Nov 27 2018
Update Date: Feb 02 2021

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.

GEN Datasets:
GEND000564
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Qiagen RNAeasy Plus Micro Kit NuGEN Ovation RNA-Seq System V2 for LCM as well as bulk samples and Illumina TruSeq RNA prep kit for bulk samples, respectively. See characteristics 'Library_method'.
Library Construction Protocol: -
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: SINGLE
Library Strand: -; Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2000
Strand-Specific: Unspecific; Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Condition Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate