NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2050619 Query DataSets for GSM2050619
Status Public on Feb 22, 2018
Title wild type A549 _No3
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
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P058197 3.2074773
ASHGA5P007773 5.9379787
ASHGA5P031162 3.4941435
ASHGA5P041796 14.692485
ASHGA5P006930 8.327297
ASHGA5P031496 8.107253
ASHGA5P050699 13.065792
ASHGA5P035298 2.5054374
ASHGA5P014867 2.5054374
ASHGA5P008172 6.0271487
ASHGA5P047663 4.0415063
ASHGA5P012016 8.113581
ASHGA5P007747 9.104679
ASHGA5P026943 2.7401328
ASHGA5P035562 5.2086854
ASHGA5P018786 10.081566
ASHGA5P001180 6.3321805
ASHGA5P023786 2.5054374
ASHGA5P021269 2.5054374
ASHGA5P000239 4.122028

Total number of rows: 58944

Table truncated, full table size 1361 Kbytes.




Supplementary file Size Download File type/resource
GSM2050619_R3.txt.gz 2.7 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap