|
| Status |
Public on Apr 14, 2013 |
| Title |
Human microvascular endothelial cell |
| Sample type |
SRA |
| |
|
| Source name |
Human microvascular endothilial cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Dermal Microvascular Endothelial Cells (Lonza)
|
| Growth protocol |
Cultured with endothelial cell growth medium-2MV (EGM-2, Lonza)
|
| 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 |
HMVEC
|
| 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 |
SRX249509 |
| BioSample |
SAMN01978507 |
