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

PRJNA326167: Human Single Cells - Local lung hypoxia determines epithelial fate decisions during alveolar regeneration

Source: NCBI / GSE83501
Submission Date: Jun 19 2016
Release Date: Jun 20 2017
Update Date: May 15 2019

Summary: Single human lung epithelial cell transcriptomes, isolated and processed via Fluidigm C1

Overall Design: Flow sorted cells from digested human lungs were captured on the Fluidigm C1 chip.

GEN Datasets:
GEND000212
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: Tissue was mechanically and enzymatically disaggregated using dispase. Single cells were then stained with antibodies and flow sorted.
Extract Protocol: Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions.
Library Construction Protocol: Libraries were prepared using Illumina Nextera XT kit per illumina^s protocols.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Unspecific
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
Local lung hypoxia determines epithelial fate decisions during alveolar regeneration.
Nature cell biology . 2017-07-24 [PMID: 28737769]