|
| Status |
Public on Jan 01, 2015 |
| Title |
HUVEC |
| Sample type |
SRA |
| |
|
| Source name |
HUVEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human umbilical vein endothelial cell
passages: 15
|
| Treatment protocol |
Human LSECs and hepatocytes were purified from normal liver cell suspension discarded during isolation of hepatocytes collected for transplantation. Briefly, liver cells were dispersed with collagenase and hepatocytes were isolated by filtration and low speed centrifugation.18 The cells remaining in the supernatant were collected and cryopreserved. In addition, LSECs at passage 1 were purchased from ScienCell (San Diego, CA) and human umbilical vein endothelial cells (HUVECs-passage 1) and hepatocytes from Promocell (Heidelberg, Germany). CHO cells transduced with an expression vector for FVIII were kindly provided by A. Benhida (University of Leuven, Belgium).19 The study was approved by the University of Louvain Ethics committee.
|
| Growth protocol |
primary cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To prepare cell extracts, the cells were pelleted by centrifugation and immediately lysed in variable amounts of CelLytic M cell lysis reagent (lysis buffer; Sigma-Aldrich) containing 1x protease inhibitor (Halt Protease inhibitor Single-use Cocktail; Thermo Scientific; Belgium) for 15 minutes on ice followed by 5 minutes centrifugation at 18,000g (13,000 rpm) at 4°C to remove the debris. The lysate was then used for further analysis.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kits v2 RS-122-2001
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HSR000328
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.6 with default settings
The abundance data was generated with cufflinks v.2.0.2 using the tool cuffcompare.
Genome_build: hg19 (NCBI Homo sapiens build 37.2)
Supplementary_files_format_and_content: the tmap files (output of cufflinks) with abundance measurements.
|
| |
|
| Submission date |
Feb 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marc Jacquemin |
| Organization name |
KU Leuven
|
| Street address |
O&N I Herestraat 49 - bus 913
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE43984 |
Transcriptome analysis of human sinusoidal endothelial cells, hepatocyte |
|
| Relations |
| SRA |
SRX221669 |
| BioSample |
SAMN01908941 |
