|
| Status |
Public on Aug 25, 2017 |
| Title |
IMM_EPA08P1_hu WB_SLE_TRD-000522_50 |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
processing_batch: Batch1
disease: SLE
sample_collection_overview: 2.5 mL of peripheral blood from SLE patients were collected directly into PAXgene tubes
|
| Treatment protocol |
PAXgene tubes were stored at -20C until processing for RNA extraction. RNA extraction and Affy profiling were performed in four different batches, noted in the experiment design.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cells with Qiagen PAXgene blood miRNA kit (Cat. # 763134).
|
| Label |
biotin
|
| Label protocol |
Total RNA was treated with DNase I and cleaned up with Qiagen RNeasy MiniElute Cleanup Kit (Cat. # 74204). The RNA concentrations were determined by NanoDrop and RNA quality was evaluated using Experion (Bio-Rad). All target labeling reagents were purchased from Affymetrix (West Sacramento CA). Double-stranded cDNAs were synthesized from 1ug of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA was generated from cDNA and used to probe Human Genome U219 array, comprising of 49,293 probe sets and representing more than 20,000 human genes
|
| Scan protocol |
Biotin-labeled cRNA was generated from cDNA and used to probe Human Genome U219 array, comprising of 49,293 probe sets and representing more than 20,000 human genes, using the Gene Titan MC instrument (Affymetrix, West Sacramento, CA). All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
|
| Data processing |
CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm using the “Affy” package in R with custom CDF from BrainArray.
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| |
|
| Submission date |
Aug 09, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Hanjoong Jo |
| E-mail(s) |
[email protected]
|
| Phone |
(404) 712-9654
|
| Organization name |
Georgia Tech and Emory Univ
|
| Department |
Coulter Department of Biomedical Engineering
|
| Street address |
1760 Haygood Drive, Health Sciences Research Bldg E170
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
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