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Sample GSM1098572 Query DataSets for GSM1098572
Status Public on Apr 14, 2013
Title iEC: Rep1
Sample type SRA
Source name Induced endothelial cell
Organism Homo sapiens
Characteristics cell type: Induced endothelial cells from cultured foreskin fibroblast cells (Stegment)
Growth protocol Fibroblasts were treated with Poly I:C (30ng/ml) and the medium changed to DMEM with 7.5% FBS and 7.5% knockout serum replacement (KSR). With daily treatments of Poly I:C for 7 days, the medium was gradually transitioned to contain 10% KSR. Cells were treated with transdifferentiation medium containing 20ng/ml bone morphogenetic protein-4 (BMP-4, Peprotech), 50ng/ml vascular endothelial growth factor (VEGF, Peprotech) and 20ng/ml basic fibroblast growth factor (bFGF, BD Bioscience) for another 7 days, with new medium every 2 days. For maintenance of transdifferentiation, the cells were cultured another 2 weeks in the presence of bFGF, VEGF and 0.1mM 8-bromoadenosine-3’:5’-cyclic monophosphate sodium salt (8-Br-cAMP, Sigma), with the medium changed every 2 days
Extracted molecule total RNA
Extraction protocol Using RNeasy Mini Kit (Qiagen), total RNA was extracted and quantitative polymerase chain reaction was performed using Taqman gene expression assays (Applied Biosystems)
RNA-Seq–based expression analysis was carried out using RNA samples converted into individual cDNA libraries using Illumina (San Diego, CA). TruSeq methods employed single reads of 50 base-lengths sequenced at 20-30 million read depths using the Illumina HiSeq 2500 instrument.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description iECa
Data processing Trimmed sequences were generated as fastq outputs and analyzed based on the TopHat/Cufflinks pipeline based on reference annotations produced by the Ensembl Gencode project. Differential and significant gene expression analysis was carried out using gene-level FPKM (fragments per kilobase of gene locus summarized mRNA per million reads) expression levels.
Gene-level expression was normalized and baselined to the 80th percentile of that sample's overall expression in GeneSpring v7.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Each sample has a corresponding .txt file with normalized FPKM
Submission date Mar 14, 2013
Last update date May 15, 2019
Contact name Rebekah Karns
Organization name Cincinnati Children's Hospital Medical Center
Department Gastroenterology, Hepatology, & Nutrition
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45276
Country USA
Platform ID GPL16791
Series (1)
GSE45176 RNA-seq expression analysis to determine expression profile similarities between fibroblasts, induced endothelial cells from fibroblasts, and human dermal microvascular endothelial cells
SRA SRX249507
BioSample SAMN01978505

Supplementary file Size Download File type/resource
GSM1098572_iECa_Processed.txt.gz 560.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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