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Sample GSM722306 Query DataSets for GSM722306
Status Public on May 10, 2011
Title Healthy Donor 1
Sample type RNA
 
Source name peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics disease state: Healthy non infected
individual: donor 1
tissue: Peripheral venous blood
cell type: peripheral blood mononuclear cells
gender: Female
age: 32y
Treatment protocol Peripheral venous blood (10 mL) was drawn from each subject and PBMCs were isolated on Ficoll gradients (GE Health Care, Little Chalfont, U.K); PBMCs were immediately mixed with the miR VanaTM miRNA isolation kit Lysis Buffer (Ambion Inc .Austin, Tx) and frozen at −80°C until RNA was extracted.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miR VanaTM miRNA isolation kit (Ambion Inc .Austin, Tx) according to the manufacturer’s instructions. RNA quantity and quality was assessed using the Nanodrop 2000 (Thermo Fisher Scientific, Mass) and Agilent 2100 bioanalyzer systems (Agilent Technologies). Samples with a RNA Integrity Number above 7 were used in the study.
Label Cy3
Label protocol 100 ng total RNA (50 ng /ul )were first treat with phosohatase (TakaRa p/n 2250A)at 37 ºC for 30 min .After adding DMSO(Sigma p/n D8418) , samples were heat at 100 ºC for 5-10 min and incubate in ice immediately .Assemble labeling reaction with pCp-Cy3 were then performed by using T4 RNA Ligase at 16ºC for 2h. labeled RNA were then purified by using the Micro Bio spin 6 columns(Bio-Rad p/n 732-6221).
 
Hybridization protocol Cy3-labelled RNAs were heat at 100 °C for 5 minutes in a reaction volume containing 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer following the manufacturers instructions. Samples were transfer to ice water baths for 5 min after and then hybridized to Agilent-021827 Human miRNA Microarray (V3) (miRBase release 12.0 miRNA ID version) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Microarray slides were scanned by using the XDR Scan (PMT100, PMT5).(Scan Area 61 x 21.6 mm ; Scan resolution 5 um; Single pass; eXtended Dynamic range selected ; Green Dye channel ; Green PMT XDR Hi 100% , XDR Lo 5% )
Description Healthy non infected donor 1
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol miRNA-v1_95_May07) to obtain background subtracted and spatially detrended Processed Signal intensities. The signal (after background subtraction) was exported directly into the GeneSpring GX9.0 software (Agilent Technologies) for quantile normalization.
 
Submission date May 10, 2011
Last update date May 10, 2011
Contact name qian gao
E-mail(s) qgao99@yahoo.com
Organization name Fudan University
Department Shanghai Medical School
Lab Key Laboratory of Medical Molecular Virology
Street address 138, Yi xue yuan Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL10850
Series (1)
GSE29190 Comparative miRNA Expression Profiles in Individuals with Latent and Active Tuberculosis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
miRNABrightCorner30 249.4675749
DarkCorner 66.18926292
hsa-miR-720 2785.321216
hsa-miR-587 1.019300568
hsa-miR-1236 1.019300568
hsa-miR-607 1.019300568
hsa-miR-1253 1.019300568
hsa-miR-369-3p 1.019300568
hsa-miR-657 1.019300568
hsa-miR-526b 1.019300568
hsa-miR-515-3p 11.75912168
hsa-miR-586 1.019300568
hsa-miR-485-5p 1.019300568
hsa-miR-507 1.019300568
hsa-miR-551b* 1.019300568
hsa-miR-326 1.019300568
hsa-miR-146b-3p 14.74273719
hsa-miR-1283 2.362128419
hsa-miR-622 1.019300568
hsa-miR-556-5p 1.019300568

Total number of rows: 961

Table truncated, full table size 23 Kbytes.




Supplementary file Size Download File type/resource
GSM722306_US252182710173_S01_miRNA_2_2.txt.gz 904.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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