|
| Status |
Public on Jun 12, 2017 |
| Title |
Scleroderma patient 1 |
| Sample type |
RNA |
| |
|
| Source name |
monocytes from scleroderma patient
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: diffuse cutaneous scleroderma (dcSSc)
cell type: monocytes
|
| Treatment protocol |
N/A
|
| Growth protocol |
Monocytes were isolated by negative depletion from the negative fraction of PBMCs depleted of CD19+ cells, using magnetic beads (easySep, StemCell).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from monocytes was extracted using an miRNeasy kit according to the manufacturer's protocol (QIAGEN, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) 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 (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression from monocytes of scleroderma patient.
|
| 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 package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0) (http://mbni.org/customcdf/17.0.0/entrezg.download/hugene20st_Hs_ENTREZG_17.0.0.zip).
|
| |
|
| Submission date |
Sep 15, 2016 |
| 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) |
| GSE86984 |
Gene expression profile in freshly isolated monocytes from patients with diffuse cutaneous scleroderma (dcSSc) compared to healthy donors (HDs) |
|
