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Sample GSM2190607 Query DataSets for GSM2190607
Status Public on Jun 30, 2016
Title DEP treated HBE_No1
Sample type RNA
 
Source name HBE cells
Organism Homo sapiens
Characteristics cell line: human bronchial epithelial (HBE) cell line
treatment: diesel exhaust particles (DEP)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
Label Cy3
Label protocol RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c,Terminated by incubation for 15 min at 65°C.
 
Hybridization protocol After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.a,The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)
Scan protocol Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).
Description R4
Data processing Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Discriminant miRNAs and differences between groups were analyzed using Bayes moderated t test (limma) with Benjamini Hochberg false discovery rate (FDR) at P < 0.05. A two-fold cut-off difference was applied to select the up- and down-regulated miRNAs.
 
Submission date Jun 07, 2016
Last update date Jun 30, 2016
Contact name Xiaobo Li
E-mail(s) 101011116@seu.edu.cn
Organization name Southeast University
Street address Dingjiaqiao 87
City Nanjing
ZIP/Postal code 210009
Country China
 
Platform ID GPL16956
Series (1)
GSE82335 Diesel exhaust particle (DEP)-treated HBE cells

Data table header descriptions
ID_REF
VALUE Median-normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P058197 4.097997
ASHGA5P007773 2.783771
ASHGA5P031162 3.991402
ASHGA5P041796 7.294649
ASHGA5P006930 4.6827793
ASHGA5P031496 3.0421402
ASHGA5P050699 6.5979047
ASHGA5P035298 2.8526313
ASHGA5P014867 3.3192194
ASHGA5P008172 3.5524826
ASHGA5P047663 2.783771
ASHGA5P012016 7.9982686
ASHGA5P007747 2.783771
ASHGA5P026943 2.783771
ASHGA5P035562 5.5461884
ASHGA5P018786 2.854564
ASHGA5P001180 3.2849295
ASHGA5P023786 4.4122033
ASHGA5P021269 5.276554
ASHGA5P000239 7.2376366

Total number of rows: 58944

Table truncated, full table size 1339 Kbytes.




Supplementary file Size Download File type/resource
GSM2190607_R4.txt.gz 2.6 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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