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Sample GSM1754615 Query DataSets for GSM1754615
Status Public on Aug 22, 2015
Title CTRL004M
Sample type RNA
 
Source name Cell specific microRNA transcriptome from blood monocytes isolated from a TB patient, female
Organism Homo sapiens
Characteristics tissue: monocytes
gender: female
study group: TB patient
matched pair id: P12
subject id: CTRL004
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 monocytes isolated from a TB patient, 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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_25_P00013722 3.425281315
A_25_P00015543 3.219602419
A_25_P00013773 3.481869104
A_25_P00015229 3.542227079
A_25_P00016018 3.074175285
A_25_P00011991 7.139857043
A_25_P00015101 3.497690902
A_25_P00010432 5.902047891
A_25_P00015836 4.744161797
A_25_P00010259 3.295007543
A_25_P00015285 4.933110808
A_25_P00015097 3.505474571
A_25_P00012376 6.139971344
A_25_P00012139 5.220084751
A_25_P00015493 3.441128353
A_25_P00012297 3.273073559
A_25_P00010683 8.678608624
A_25_P00015031 3.472352928
A_25_P00015444 3.770371222
A_25_P00012542 3.525359113

Total number of rows: 3523

Table truncated, full table size 92 Kbytes.




Supplementary file Size Download File type/resource
GSM1754615_US22502595_253118113314_S01_miRNA_1100_Jul11_1_1.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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