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Sample GSM2190608 Query DataSets for GSM2190608
Status Public on Jun 30, 2016
Title DEP treated HBE_No2
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 R5
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 2.8028946
ASHGA5P007773 2.8068826
ASHGA5P031162 4.169779
ASHGA5P041796 7.372927
ASHGA5P006930 3.733111
ASHGA5P031496 2.8673136
ASHGA5P050699 6.922745
ASHGA5P035298 3.7448366
ASHGA5P014867 3.0913897
ASHGA5P008172 4.3732195
ASHGA5P047663 2.9285994
ASHGA5P012016 7.370644
ASHGA5P007747 2.9426544
ASHGA5P026943 2.9472451
ASHGA5P035562 6.2812924
ASHGA5P018786 4.230554
ASHGA5P001180 4.9416513
ASHGA5P023786 5.082875
ASHGA5P021269 5.315108
ASHGA5P000239 7.8602424

Total number of rows: 58944

Table truncated, full table size 1361 Kbytes.




Supplementary file Size Download File type/resource
GSM2190608_R5.txt.gz 2.8 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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