|
| Status |
Public on Jul 18, 2019 |
| Title |
31.Placebo.LS.Day1 |
| Sample type |
RNA |
| |
|
| Source name |
Skin biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
patient_id: 31
batch_date: 2018-01-24
tissue: LS
week: Day1
treatment: Placebo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin biopsies from lesional and non-lesional skin at baseline, day15 and day29 were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).
|
| Label |
biotin
|
| Label protocol |
Ovation WB Reagent (Nugen)
|
| |
|
| Hybridization protocol |
Affymetrix Human U133Plus 2.0 gene arrays were used. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, CA). The labeled target was fragmented and hybridized to probe gene arrays, using Encore Biotin Module from NuGen (San Carlos, CA). The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, CA). On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.
|
| Scan protocol |
Hewlett-Packard GeneArray Scanner G2500A
|
| Description |
Gene expression data from skin biopsy
|
| Data processing |
Quality control of Affymetrix chips was done using standard QC metrics and R packages. Expression measures were obtained using GC Robust Multi-array Average (GCRMA) algorithm. Batch effects corresponding to the hybridization date were detected by principal component analyses and adjusted using ComBat algorithm from R’s sva package. Probe sets with expression >3 in at least 15 samples were used for further analyses. Gene expression changes were modeled using mixed-effect models, with treatment, time and tissue type as a fixed interaction term, and a random effect for each patient. Fold changes (FCHs) for the comparisons of interest were estimated, and hypothesis testing was conducted with contrasts under the general framework of linear models in the R limma package. P-values were adjusted for multiple hypotheses using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).
|
| |
|
| Submission date |
Jun 26, 2019 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Ana Pavel |
| E-mail(s) |
anabrandusa@gmail.com
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Dermatology
|
| Street address |
One Gustave L. Levy Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE133385 |
Oral JAK/SYK-inhibition (ASN002) suppresses inflammation and improves epidermal barrier markers in atopic dermatitis |
|
