Experiment Detail
| Title | Illumina HiSeq 2500 paired end sequencing; Transcriptome analysis of HUVEC |
| Design Description | Transcriptome analysis of HUVEC |
| Organism | Homo sapiens |
Library Description
| Name | Sample 2_p |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | RANDOM |
| Layout | PAIRED |
| Orientation | |
| Nominal Length | 500 |
| Nominal Sdev | 300 |
| Construction Protocol | Human umbilical vein endothelial cells (HUVEC) were isolated from umbilical cords from four different donors, as previously described (Cooke, B.M., Usami, S., Perry, I., and Nash, G.B. (1993). A Simplified Method for Culture of Endothelial-Cells and Analysis of Adhesion of Blood-Cells under Conditions of Flow. Microvasc Res 45, 33-45) Cells were maintained in Medium 199 (M199, Invitrogen) containing 20% fetal calf serum, 28μg/ml gentamycin, 2.5μg/ml amphotericin B, 1ng/ml epidermal growth factor and 1μg/ml hydrocortisone (all from Sigma) for 48 hours prior to processing. HUVEC cultures isolated using this method were 96-98% pure, determined by positive staining by flow cytometry of CD105, CD31 and vWF and the expression of elevated levels of intracellular adhesion molecule (ICAM-1) and E-selectin following stimulation with the inflammatory cytokine interleukin-1β. Total HUVEC RNA was isolated using the RNeasy mini kit with QIAshredder (Qiagen) according to the manufacturer’s instructions. RNA integrity number was >8.0 for all samples. Libraries were prepared using Illumina TruSeq RNA Library Preparation Kit v2, with poly-A enrichment |
Platform
| Platform | ILLUMINA |
| Instrument Model | Illumina HiSeq 2500 |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 202 |
Read Spec
| Read Index 0 | |
|---|---|
| Read Label | |
| Read Class | Application Read |
| Read Type | Forward |
| Base Coord | 1 |
| Read Index 1 | |
| Read Label | |
| Read Class | Application Read |
| Read Type | Reverse |
| Base Coord | 102 |
Navigation
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Submission | ERA673930 |
 FTP
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Study | ERP016418 | ||
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Sample | ERS1242780 | ||
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Run | ERR1524381 |
FASTQ
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SRA
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