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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PRJNA589287

PRJNA589287: Single-Cell RNA-Seq Analysis of Metastasis-Primary Tumor Dissimilarity in a Patient with Gastrointestinal Neuroendocrine Cancer

Source: NCBI / GSE140312
Submission Date: Nov 13 2019
Release Date: Feb 01 2020
Update Date: Apr 13 2020

Summary: A 58 year old female diagnosed with a metastic GI-NET underwent resection of primary tumor as well as several metastatic lesions. We performed scRNA-seq of the primary tumor and one lesion from the liver metastasis to perform comparitive analysis between the primary and metastic tumor compositions.

Overall Design: scRNAseq was performed on theprimary small intestinal neuroendocrine tumor and its matched liver metastasis simultaneously.

GEN Datasets:
GEND000122
Strategy:
Species:
Tissue:
Healthy Condition:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Both primary neuroendocrine tumor and metastatic liver lesion were processed simulatneously, to avoid batch effects. Single cell suspensions were prepared via both mechanical and enzymatic digestion protocols (collagenase I, DNAseI and TrpLE) .Viable cell count was determined using trypan blue exclusion and a total of 10,000 cells per sample were loaded onto the 10X microfluidic chip. mRNA from individual cells were captured and tagged with barcodes using 10X-Genomics microfluidic platform. cDNA was then prepared in the encapsulated gel bead emulsion and the emsulion was broken for further library preparation.
Library Construction Protocol: Barcoded cDNA libraries were prepared according to manufacturer's instructions, 10X Genomics.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 4000
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
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 Case Detail Control 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
Publications
Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis-specific targets in a patient with small intestinal neuroendocrine cancer.
Cold Spring Harbor molecular case studies . 2020-04-01 [PMID: 32054662]