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| Status |
Public on Apr 14, 2013 |
| Title |
iEC: Rep2 |
| Sample type |
SRA |
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| Source name |
Induced endothelial cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Induced endothelial cells from cultured foreskin fibroblast cells (Stegment)
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
iECb
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| 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
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| Submission date |
Mar 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rebekah Karns |
| E-mail(s) |
Rebekah.Karns@cchmc.org
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| Organization name |
Cincinnati Children's Hospital Medical Center
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| Department |
Gastroenterology, Hepatology, & Nutrition
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| Street address |
3333 Burnet Ave
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45276 |
| Country |
USA |
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| 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 |
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| Relations |
| SRA |
SRX249508 |
| BioSample |
SAMN01978506 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1098573_iECb_Processed.txt.gz |
558.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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