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Sample GSM2914988 Query DataSets for GSM2914988
Status Public on Apr 01, 2018
Title WT_6.cDNA.004.C90
Sample type SRA
 
Source name Human dermal fibroblasts
Organism Homo sapiens
Characteristics disease: wild-type control
cell type: Fibroblast
passage number: P5
c1 chip size: Large
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).
Extracted molecule total RNA
Extraction protocol Fibroblasts were collected by trypsinization and resuspended in 5 ul of fibroblast medium for loading into the C1 capture chip.
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 (Illumina) according to the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing Reads were mapped to hg19 using Bowtie2 (version 2.2.4) and Tophat (version 2.0.9)
Two single-cell samples sequenced as population controls with high read counts were sub-sampled (random sub-sampling, 10% of total reads)
Gene expression levels were calculated using Cuffquant (Cufflinks version 2.2.1 with parameters -u -max-bundle-frags 10000000) and Cuffnorm (Cufflinks version 2.2.1)
FPKM values as estimated by Cufflinks were added a value of 1 (to avoid zeros) and log2 transformed
Lowly expressed genes (average log2 (FPKM) < 1.5) were excluded from further analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimted text file includes FPKM values
 
Submission date Jan 08, 2018
Last update date Apr 01, 2018
Contact name Jakub Tolar
E-mail(s) [email protected]
Organization name University of Minnesota, Twin Cities
Department Pediatrics
Street address 420 Delaware St SE
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
 
Platform ID GPL15520
Series (1)
GSE108849 Single-cell RNA-seq of fibroblasts from recessive dystrophic epidermolysis bullosa patients and wild-type controls
Relations
BioSample SAMN08325609
SRA SRX3583912

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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