|
| Status |
Public on May 02, 2014 |
| Title |
ECFC_Scramble_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Human primary endothelial colony-forming cells
|
| Organism |
Homo sapiens |
| Characteristics |
source: ECFCs derived from umbilical cord blood
treatment: Scramble shRNA
|
| Treatment protocol |
Paired samples were infected with lentiviruses expressing an anti-TAL1 shRNA or a scrambled shRNA as a negative control. Infection was done at a multiplicity of infection (MOI) of 100 twice at 24 hours interval in presence of 4μg/ml Hexadimethrine bromide.
|
| Growth protocol |
Human umbilical cord blood from normal full-term deliveries were obtained after informed consent. Light-density mononuclear cell (MNC) fractions were isolated by Ficoll density and resuspended in complete EGM-2 medium (EBM-2 Endothelial Cell basal Medium-2, Lonza, Cat# CC-3156, supplemented with EGM-2 SingleQuot Kit Supplements & Growth Factors, Lonza, Cat# CC-4176) and 10% fetal bovine serum and plated on to CellBIND 6 well plates at 1x10^7 cells/well. Individual ECFC colonies were isolated with 0.05% trypsin and expanded in EGM-2 medium. ECFCs at passage 3 were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA-free total RNA was isolated with the RNeasy Mini Kit following the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Affymetrix standard protocol for GeneChip Whole Transcript Expression Arrays. Labeling performed at the StemCore Laboratories Affymetrix Microarray facility at the Ottawa Hospital Research Institute (Ottawa, Ontario, Canada).
|
| |
|
| Hybridization protocol |
Affymetrix standard protocol for GeneChip for cartridge arrays. Hybridization performed at the StemCore Laboratories Affymetrix Microarray facility at the Ottawa Hospital Research Institute (Ottawa, Ontario, Canada)
|
| Scan protocol |
Affymetrix standard protocol for GeneChip for cartridge arrays. Scan performed at the StemCore Laboratories Affymetrix Microarray facility at the Ottawa Hospital Research Institute (Ottawa, Ontario, Canada).
|
| Description |
Gene expression of Endothelial Colony Forming-Cell treated with a scramble shRNA
|
| Data processing |
CEL files were imported into R/Bioconductor package 'affy'. The data was normalized using the RMA algorithm. Probes with variance under the 25th quantile were removed. Differential expression analysis was performed with the R/Bioconductor 'limma' package. Probes with Benjamini-Hochberg adjusted p-value lower than 0.05 were deemed as significant.
|
| |
|
| Submission date |
Feb 20, 2013 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Marjorie Brand |
| E-mail(s) |
karthi.sivaraman@gmail.com, mbrand@ohri.ca
|
| Organization name |
Ottawa Hospital Research Institute
|
| Street address |
501 Smyth Road
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE44444 |
shRNA mediated knock-down of Tal1 in human Endothelial Colony Forming Cells (ECFCs) |
| GSE44546 |
TAL1 in human Endothelial Colony-Forming Cells |
|
| Relations |
| Reanalyzed by |
GSE86357 |
