|
| Status |
Public on Dec 25, 2018 |
| Title |
Donor 2 - CTR |
| Sample type |
RNA |
| |
|
| Source name |
ASM cells_control
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: Donor 2
cell type: airway smooth muscle (ASM) cells
culture condition: control medium (CTR)
treatment: CTR
|
| Treatment protocol |
Cells were cultured in control medium (CTR) or medium containing a pan-RA receptor inhibitor BMS 493 (10-6M) for 24 hours.
|
| Growth protocol |
De-identified primary human ASM cells, provided by Gift of Hope Foundation (Itasca, IL) were cultured in 75 cm2 culture flasks containing DMEM/F12 supplement with 10% FBS, 1x antibiotic/antimycotic mixture to 80% confluency. Cells from each donor were counted and split into four wells of 22,000 cells per well and cultured
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA using Rneasy Mini Kit (Qiagen) 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 Array 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 |
SAMPLE 3
|
| 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 |
Jul 10, 2018 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE116845 |
Expression data from retinoic acid-sufficient and retinoic acid-deficient human airway smooth muscle [human primary ASMs] |
|
