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

PRJNA428940: Single-cell RNA-seq of fibroblasts from recessive dystrophic epidermolysis bullosa patients and wild-type controls

Source: NCBI / GSE108849
Submission Date: Jan 08 2018
Release Date: Apr 1 2018
Update Date: May 22 2019

Summary: The goal of this study is to discover fibroblast subpopulations relevant to recessive dystrophic epidermolysis bullosa

Overall Design: Cultured fibroblasts from recessive dystrophic epidermolysis bullosa patients and wild-type controls were captured using the C1 Fluidigm and sequenced on an Illumina MiSeq

GEN Datasets:
GEND000036
Strategy:
Species:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: Dermal fibroblasts from patients with recessive dystrophic epidermolysis bullosa and their human leukocyte antigen (HLA) matched healthy siblings were obtained from skin biopsies and cultured in DMEM high glucose (Thermo Fisher Scientific) containing 10% fetal bovine serum (MilliporeSigma), 1% Pen/Strep (Thermo Fisher Scientific), 1% L-glutamine (Thermo Fisher Scientific), and 1% MEM NEAA (Thermo Fisher Scientific). For sub-culture, the medium was removed and cells were washed with 1X PBS (Thermo Fisher Scientific) and detached using Trypsin/EDTA (Thermo Fisher Scientific).; Dermal fibroblasts from patients with recessive dystrophic epidermolysis bullosa and their human leukocyte antigen (HLA) matched healthy siblings were obtained from skin biopsies and cultured in DMEM high glucose (Thermo Fisher Scientific) containing 10% fetal bovine serum (MilliporeSigma), 1% Pen/Strep (Thermo Fisher Scientific), 1% L-glutamine (Thermo Fisher Scientific), and 1% MEM NEAA (Thermo Fisher Scientific). For sub-culture, the medium was removed and cells were washed with 2X PBS (Thermo Fisher Scientific) and detached using Trypsin/EDTA (Thermo Fisher Scientific).; Dermal fibroblasts from patients with recessive dystrophic epidermolysis bullosa and their human leukocyte antigen (HLA) matched healthy siblings were obtained from skin biopsies and cultured in DMEM high glucose (Thermo Fisher Scientific) containing 10% fetal bovine serum (MilliporeSigma), 1% Pen/Strep (Thermo Fisher Scientific), 1% L-glutamine (Thermo Fisher Scientific), and 1% MEM NEAA (Thermo Fisher Scientific). For sub-culture, the medium was removed and cells were washed with 3X PBS (Thermo Fisher Scientific) and detached using Trypsin/EDTA (Thermo Fisher Scientific).
Treatment Protocol: -
Extract Protocol: Fibroblasts were collected by trypsinization and resuspended in 5 ul of fibroblast medium for loading into the C1 capture chip.
Library Construction Protocol: cDNA was created from selected cells using the SMARTer Ultra Low RNA kit designed for the C1 system (Clontech). mRNA libraries were constructed using the the Nextera XT kit (Illumi-) according to the manufacturer protocol.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina MiSeq
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
A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.
PLoS computational biology . 2018-04-09 [PMID: 29630593]