|
| Status |
Public on Feb 01, 2017 |
| Title |
Neutrophils, Patient, JIA, ID, Biological replicate 9 [RNA] |
| Sample type |
RNA |
| |
|
| Source name |
neutrophil RNA, JIA, ID
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: juvenile idiopathic arthritis (JIA)
group: inactive disease, on therapy (ID)
cell type: neutrophils
|
| Treatment protocol |
Peripheral blood mononuclear cells (PBMCs) were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr on Affymetrix human EXON 1.0 ST array or GeneChip™ miRNA 1.0 array following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix 3000 7G scanner.
|
| Description |
J55JJ
|
| Data processing |
Expression summary values from Affymetrix Exon and miRNA arrays were generated using RMA software in the Affy package of Bioconductor in the R statistical computing environment.
|
| |
|
| Submission date |
Jan 31, 2017 |
| Last update date |
Feb 01, 2017 |
| Contact name |
kaiyu Jiang |
| Organization name |
University at Buffalo
|
| Department |
Pediatrics
|
| Street address |
875 Ellicott Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE94354 |
Modeling Transcriptional Rewiring in Neutrophils through the Course of Treated Juvenile Idiopathic Arthritis |
|
