|
| Status |
Public on Apr 24, 2013 |
| Title |
Patient 4, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0] |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: relapsing-remitting multiple sclerosis
gender: female
age at ifn-beta therapy onset (baseline blood sampling): 50
duration from diagnosis to therapy initiation (in months): 12
edss at baseline: 2.5
edss after 1 year: 2.5
edss after 2 years: 5.5
number of relapses during the year prior to treatment: 0
number of relapses during 1-year follow-up: 0
number of relapses during 2-year follow-up: 0
completed years of ifn-beta therapy: 21
|
| Treatment protocol |
Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer HealthCare) at standard doses.
|
| Growth protocol |
Patient blood samples were taken immediately before first IFN-beta injection as well as two days, four days and one month post therapy initiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells were separated using isopycnic centrifugation (Ficoll), and total RNA enriched with small RNAs was isolated using the mirVana miRNA isolation kit (Invitrogen) according to the manufacturers' protocols.
|
| Label |
FAM dye
|
| Label protocol |
Total RNA (120 ng) was reverse transcribed to cDNA using Megaplex RT Primers in combination with Megaplex PreAmp Primers for preamplification (Life Technologies). The real-time PCRs were performed with predesigned primers and TaqMan probes in 384-well plates with 45 cycles according to the manufacturer's instructions in a 7900HT Sequence Detection System (Applied Biosystems).
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
MS4_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta
|
| Data processing |
Raw threshold cycle (Ct) values were computed using the SDS 2.3 and RQ Manager 1.2 software (Applied Biosystems), and undetermined data were set to Ct=45. To normalize the data, we first set the detection limit at Ct=38, and then converted the data to the linear scale using the equation 2^(-Ct)*10^9. Systematic differences in the time-course data of each patient were corrected by loess normalization using the R package affy. Finally, to reduce differences between the patients, we scaled the data so that the 95% quantile is the same for each patient.
Matrix non-normalized worksheet reports the raw Ct values. Matrix normalized worksheet reports the normalized expression data. Fold Change worksheet reports the log2 ratios of the microRNA expression levels during therapy compared to the pre-treatment levels (baseline).
|
| |
|
| Submission date |
Apr 22, 2013 |
| Last update date |
Aug 06, 2013 |
| Contact name |
Michael Hecker |
| E-mail(s) |
michael.hecker@rocketmail.com
|
| Organization name |
University of Rostock
|
| Department |
Department of Neurology
|
| Lab |
Division of Neuroimmunology
|
| Street address |
Gehlsheimer Str. 20
|
| City |
Rostock |
| ZIP/Postal code |
18147 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13328 |
| Series (2) |
| GSE46283 |
Expression data of multiple sclerosis patients receiving Interferon-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0] |
| GSE46293 |
Expression data of multiple sclerosis patients receiving Interferon-beta therapy |
|
