|
| Status |
Public on Jul 19, 2020 |
| Title |
Patient X38 1 Week before Omalizumab Treatment |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
diagnosis: asthma
Sex: Female
age: 19
omalizumab responder status: Responder
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated utilizing MagMax Nucleic Acid Isolation kit (Ambion) according to manufacturer's protocol. Globin mRNA was removed with using Globin Clear kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
1500ng of RNA from each sample that passed quality control was amplified and labled using Illumina TotalPrep RNA Amplification kit following manufacturer's protocol
|
| |
|
| Hybridization protocol |
Amplified and labeled RNA was hybridized overnight to beadchips following standard Illumina protocol
|
| Scan protocol |
Scanned on Illumina HiScan following standard Illumina protocol
|
| Description |
raw data file:
Non-normalized_data_2.txt
X38W-1
Former smoker
|
| Data processing |
Each sample was background subtracted and scaled to the average of all samples. Raw values less than 10 were set to 10 and the data was log2 transformed. Probes were then filtered to select transcripts that were present in at least one sample (PALO) using an alpha of 0.01 for the signal detection, thus eliminating background. The probes were then additionally filtered by removing probes with the lowest variability using a standard deviation of less than 0.344.
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Jul 19, 2020 |
| Contact name |
Sangkon Oh |
| Organization name |
Mayo Clinic
|
| Department |
immunology
|
| Lab |
oh lab
|
| Street address |
13400 east Shea street
|
| City |
Scottsdale |
| State/province |
AZ |
| ZIP/Postal code |
85259 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE134544 |
Whole blood transcriptional variations between responders and non-responders in asthma patients receiving omalizumab |
|
