|
| Status |
Public on Aug 22, 2015 |
| Title |
TB001N |
| Sample type |
RNA |
| |
|
| Source name |
Cell specific microRNA transcriptome from blood granulocytes isolated from a household contact, female
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: granulocytes
gender: female
study group: household contact
matched pair id: P14
subject id: TB001
|
| Treatment protocol |
Patients presenting with TB symptoms (TB, n=8) were recruited on the day of diagnosis, and subsequently, LTBI participants (LTBI, n=8) were recruited to match the patients' age and gender. Granulocytes and monocytes were sequentially separated from peripheral blood by magnetic beads (MACS, Miltenyi Biotec GmbH, CD15+ and CD14+, respectively) according to manufacturer's instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (tRNA) was isolated using TRIzol® reagent (Life Technologies Corporation) according to manufacturer's instructions. Quality and quantisty of nucleic acids were determined by electrophoresis and spectrophotometry.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labeled with the single-color Quick amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
After precipitation, purification and quantification of the labeling reactions, 1.25µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies). Washing of the hybridizations was done with the SSPE wash protocol according to the supplier's protocol (Agilent Technologies).
|
| Scan protocol |
Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).
|
| Description |
Cell specific microRNA transcriptome from blood granulocytes isolated from a household contact, female
|
| Data processing |
Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.0.1.1, Agilent Technologies) using the protocol GE1_1100_Jul11 according the supplier's recommendations. The raw intensity files were read into limma / BioConductor, background corrected using the normexp method and normalized using the quantile method. Intensities were averaged for identical probes and control probes were removed.
|
| |
|
| Submission date |
Jul 01, 2015 |
| Last update date |
Jan 06, 2023 |
| Contact name |
January 3rd Weiner |
| E-mail(s) |
january.weiner@gmail.com
|
| Phone |
030450543049
|
| Organization name |
Berlin Institute of Health, Charité Medical University of Berlin
|
| Department |
CUBI
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15159 |
| Series (2) |
| GSE70425 |
Cell-specific microRNA expression patterns in TB patients and household contacts |
| GSE70478 |
Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers |
|
