|
Status |
Public on Apr 14, 2013 |
Title |
Fibroblast |
Sample type |
SRA |
|
|
Source name |
Fibroblast
|
Organism |
Homo sapiens |
Characteristics |
cell type: Cultured foreskin fibroblast cells (Stegment)
|
Growth protocol |
Cultured in DMEM with 10% FBS and 1% penicillin/streptomycin (5% CO2, 37°C)
|
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 |
Fibro
|
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 |
E-mail(s) |
Rebekah.Karns@cchmc.org
|
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 |
|
Relations |
SRA |
SRX249510 |
BioSample |
SAMN01978508 |