|
| Status |
Public on May 18, 2024 |
| Title |
SCR 1 |
| Sample type |
RNA |
| |
|
| Source name |
lymphatic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphatic cells
sirna: scrambled siRNA
|
| Treatment protocol |
The cells were transfected with 10 nM of scrambled siRNA (siSCR), siRNA against ERG (siERG), siRNA against FLI1 (siFLI1), or siRNAs against both siERG and siFLI1 (siEF) using Invitrogen™ Lipofectamine™ RNAiMAX Transfection Reagent for 24 hours.
|
| Growth protocol |
The cells were grown and maintained in Endothelial Cell Basal Medium MV2 with supplements (PromoCell, Heidelberg, Germany) until they reached 70% confluency
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 24-hour transfection, total RNAs were extracted with Trizol according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from lymphatic cells treated with scrambled siRNA.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).
|
| |
|
| Submission date |
May 13, 2024 |
| Last update date |
May 18, 2024 |
| Contact name |
Maria Trojanowska |
| E-mail(s) |
trojanme@bu.edu
|
| Phone |
6173587697
|
| Organization name |
Boston University
|
| Department |
Arthritis and Autoimmune Diseases Research Center
|
| Lab |
Trojanowska Lab
|
| Street address |
75 E. Newton St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE267348 |
Deficiency of lymphatic ERG and FLI1 in systemic sclerosis is associated with rarefaction of skin blood and lymphatic vasculature |
|
