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Sample GSM2264305 Query DataSets for GSM2264305
Status Public on Aug 10, 2016
Title sample6: FBs cultured in Lum
Sample type SRA
 
Source name dermal fibroblasts
Organism Mus musculus
Characteristics background strain: C57BL/6
cell type: dermal fibroblast of adult skin
passages: P3-5
Treatment protocol Fibroblasts were cultured with the indicated proteins (the concentration of each protein was 0.01 μg/ml) or E16.5 skin extract (2 μg/ml) for 3 days.
Growth protocol All fibroblasts and DP cells were expanded and cultured in DMEM with 10% FBS
Extracted molecule total RNA
Extraction protocol Totoal RNA was extracted using Qiagen RNeasy kit(Cat No./ID: 74104) according to the manufacturer's protocol
Total 1~2 g RNA was purified by using poly-T oligo-attached magnetic beads.The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Paired-end 150 nucleotide reads from each mRNA library were obtained using NextSeq500 (Illumina Inc., CIC bioGUNE, Bilbao, Spain).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing RNA-seq reads were aligned to mm10 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Aug 08, 2016
Last update date May 15, 2019
Contact name Mai-Yi Fan
E-mail(s) s.maiyifan@gmail.com
Organization name National Taiwan University
Street address No1, Sec. 1, Jen - Ai Rd.
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL19057
Series (1)
GSE85303 RNAseq changes in fibroblasts after treatment with selected protein(s) or E16.5 skin extract
Relations
BioSample SAMN05513557
SRA SRX2006708

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

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