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
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Healthy Condition: |
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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. |
Molecule Type: | poly(A)+ RNA |
Library Source: | |
Library Layout: | PAIRED |
Library Strand: | - |
Platform: | ILLUMINA |
Instrument Model: | Illumina MiSeq |
Strand-Specific: | Unspecific |
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 |
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