|
| Status |
Public on Jul 07, 2017 |
| Title |
SGF treated R397W, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
SGF treated R397W
|
| Organism |
Homo sapiens |
| Characteristics |
cell: CD4+ T cell
lentivirally transduced with: R397W FOXP3
activated with: 0.5 μg/ml of phytohemagglutinin (PHA) in the presence of SGF003 (8 μg/mL)
|
| Treatment protocol |
Resting transduced T cells were activated with PHA with or without SGF.
|
| Growth protocol |
Transduced T cells were expanded in exvivo-15 medium with 5% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNEasy Mini kit according to the manufacturer's suggested protocol. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).
|
| |
|
| Hybridization protocol |
3.5µg DNA target was hybridized on GeneChip® Clariom S Human (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).
|
| Scan protocol |
The microarrays were scanned on a GeneChip® scanner 3000 (Affymetrix).
|
| Description |
Gene expression from R397W FOXP3 transduced human CD4+ T cells treated with SGF
RW-SGF-2
|
| Data processing |
The data were analyzed using R with the pd.clariom.s.human, clariomshumantranscriptcluster.db, oligo, limma and gplots packages. RMA normalization and Log2 transformation were applied to the raw intensity values.
|
| |
|
| Submission date |
May 23, 2017 |
| Last update date |
Jan 31, 2019 |
| Contact name |
Steven Shao |
| E-mail(s) |
[email protected]
|
| Organization name |
McGill University
|
| Street address |
2155 Guy Street, suite 500
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3H 2R9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24324 |
| Series (1) |
| GSE99236 |
Transcriptional changes induced in human CD4+ cells upon ectopic expression of FOXP3 |
|
