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Sample GSM1313403 Query DataSets for GSM1313403
Status Public on Apr 25, 2014
Title ADF04DF RNA-Seq
Sample type SRA
Source name normal primary dermal fibroblasts
Organism Homo sapiens
Characteristics cell line: --
cell type: normal primary dermal fibroblasts
Biomaterial provider Norwegian Stem Cell Center
Treatment protocol Cells were cultured as described under Growth protocol. 2x10e6 cells were cultured to confluency for RNA preparation before harvesting to ensure consistency of cell cycle stages between the two cell types.
Growth protocol Human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs) were cultured in DMEM/F12 containing 13% FCS, 2 ng/ml basic fibroblast growth factor and antibiotics. Cells were exponentially growing and used at passage 5-7. AD04DFs were obtained with Norwegian Ethics Committee Approval REK2617A.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing reads aligned with tophat v2.0.8b with parameter –no-novel-juncs
transcript abundance estimated with cufflinks v2.1.1 with parameter –GTF
csv file created from column 5 and 10 from cufflinks output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value
Submission date Jan 23, 2014
Last update date May 15, 2019
Contact name Philippe Collas
Organization name University of Oslo
Department Institute of Basic Medical Sciences
Street address PO Box 1112 Blindern
City Oslo
ZIP/Postal code 0317
Country Norway
Platform ID GPL16791
Series (2)
GSE54333 EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq]
GSE54334 EDD: a program for detection of wide genomic enrichment domains robust against local variations
BioSample SAMN02595207
SRA SRX447391

Supplementary file Size Download File type/resource
GSM1313403_HSF_AD04_fpkm.csv.gz 347.8 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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