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Sample GSM1754604 Query DataSets for GSM1754604
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., 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
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
VALUE Normalized signal intensity

Data table
A_25_P00013722 3.382781386
A_25_P00015543 3.174858966
A_25_P00013773 3.580790059
A_25_P00015229 3.575188766
A_25_P00016018 3.428401528
A_25_P00011991 6.552602576
A_25_P00015101 3.185039757
A_25_P00010432 5.643750468
A_25_P00015836 4.824612579
A_25_P00010259 3.27068011
A_25_P00015285 4.517974686
A_25_P00015097 3.506758565
A_25_P00012376 5.390444407
A_25_P00012139 5.005657187
A_25_P00015493 3.494602877
A_25_P00012297 3.018101277
A_25_P00010683 8.266266683
A_25_P00015031 3.540855317
A_25_P00015444 3.790113625
A_25_P00012542 3.64366847

Total number of rows: 3523

Table truncated, full table size 92 Kbytes.

Supplementary file Size Download File type/resource
GSM1754604_US22502595_253118112445_S01_miRNA_1100_Jul11_1_3.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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