|
| Status |
Public on Dec 13, 2016 |
| Title |
JNCL untreated fibroblasts [B3] |
| Sample type |
RNA |
| |
|
| Source name |
Human fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Untreated
|
| Treatment protocol |
Control and JNCL fibroblasts were treated with 100 mM of trehalose for 4 days.
|
| Growth protocol |
Control and JNCL fibroblasts were growth in DMEM with10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three hundred nanograms of total RNA were amplified and purified using Illumina TotalPrep RNA Amplification Kit (Ambion, cat# IL1791) following kit instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was synthesized by 14-hour amplification with dNTP mix containing biotin-dUTP and T7 RNA polymerase.
|
| |
|
| Hybridization protocol |
An aliquot of 750 nanograms of amplified products were loaded onto Illumina Sentrix Beadchip Array human HT12_v4 arrays, hybridized at 58ºC in an Illumina Hybridization Oven (Illumina, Cat# 198361) for 17 hours, washed and incubated with straptavidin-Cy3 to detect biotin-labeled cRNA on the arrays.
|
| Scan protocol |
After hybridization arrays were dried and scanned with BeadArray Reader (Illumina, CA)
|
| Description |
replicate3
|
| Data processing |
Data were analyzed using GenomeStudio software (Illumina, CA). Clustering and pathway analysis were performed with GenomeStudio and Ingenuity Pathway Analysis (Ingenuity Systems, Inc.) softwares respectively.
|
| |
|
| Submission date |
Jan 07, 2016 |
| Last update date |
Dec 13, 2016 |
| Contact name |
Marco Sardiello |
| E-mail(s) |
sardiell@bcm.edu
|
| Phone |
8328248871
|
| Organization name |
Baylor College of Medicine at Neurological Research Institute Texas Children Hospital
|
| Department |
Molecular and Human Genetics
|
| Lab |
Sardiello
|
| Street address |
1250 Moursund St.
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL14951 |
| Series (1) |
| GSE76643 |
Genome-wide analysis of trehalose-responsive gene expression in control or JNCL human fibroblasts. |
|
