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Sample GSM2050621 Query DataSets for GSM2050621
Status Public on Feb 22, 2018
Title Al2O3 nanoparticle treated A549_No2
Sample type RNA
Source name A549 cells
Organism Homo sapiens
Characteristics cell line: A549
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).
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 Jan 28, 2016
Last update date Feb 22, 2018
Contact name Shizhi Wang
Organization name Southeast University
Department Key Laboratory of Environmental Medicine Engineering, Ministry of Education
Street address 87 Dingjiaqiao, Gulou District
City Nanjing
State/province Jiangsu
ZIP/Postal code 210009
Country China
Platform ID GPL16956
Series (1)
GSE77355 mRNA expression profile in Al2O3 nanoparticle treated A549 cells

Data table header descriptions
VALUE Normalized signal intensity

Data table
ASHGA5P058197 2.5046096
ASHGA5P007773 6.407753
ASHGA5P031162 2.5046096
ASHGA5P041796 14.881978
ASHGA5P006930 8.6408205
ASHGA5P031496 8.095242
ASHGA5P050699 13.209075
ASHGA5P035298 2.9242187
ASHGA5P014867 2.5046096
ASHGA5P008172 6.4331136
ASHGA5P047663 4.414343
ASHGA5P012016 8.208605
ASHGA5P007747 9.134136
ASHGA5P026943 3.068682
ASHGA5P035562 4.6810923
ASHGA5P018786 9.925059
ASHGA5P001180 6.770707
ASHGA5P023786 6.449104
ASHGA5P021269 5.3569436
ASHGA5P000239 3.4338992

Total number of rows: 58944

Table truncated, full table size 1361 Kbytes.

Supplementary file Size Download File type/resource
GSM2050621_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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