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Sample GSM678292 Query DataSets for GSM678292
Status Public on Sep 01, 2011
Title 8545RA
Sample type RNA
 
Channel 1
Source name 8545RA
Organism Homo sapiens
Characteristics tissue: Reflected Amnion
labor status: term no labor TNL
Extracted molecule total RNA
Extraction protocol Amnion tissues were liquid nitrogen-pulverized using a mortar and pestle, and total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA), and treated with DNase. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE).
Label Hy3
Label protocol The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 0.3 µg total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
 
Channel 2
Source name common reference
Organism Homo sapiens
Characteristics tissue: pooled reflected and placental amnions (pool of all samples in this study)
Extracted molecule total RNA
Extraction protocol Amnion tissues were liquid nitrogen-pulverized using a mortar and pestle, and total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA), and treated with DNase. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE).
Label Hy5
Label protocol The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 0.3 µg total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
Scan protocol After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).
Description Placental amnion and reflected amnion were obtained from singleton placentas of patients at term with no labor (TNL; n=5) and in labor (TIL; n=5). Approximately a quadrant of placental amnion was sampled in each placenta by blunt dissection. Reflected amnion samples were taken from regions at least 2 cm apart from the rupture sites and the placental margin, also by blunt dissection.
Data processing The quantified signals were background corrected (Normexp with offset value 0 – Ritchie et al., 2007, Bioinformatics (2007), Vol. 23 no. 20) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. These steps were performed using the limma package of Bioconductor using the R language (2.12.1). Normalized Log2 Hy3/Hy5 values were averaged over all spots corresponding to a unique miRNA. Only miRNAs with 2 or more spots having a foreground signal greater than background were considered present in a given sample. miRNAs not present in at least 4 samples were not considered for differential expression analysis.
 
Submission date Feb 22, 2011
Last update date Sep 01, 2011
Contact name Adi Tarca
E-mail(s) atarca@med.wayne.edu
Phone 3135775305
Organization name Wayne State University
Department Perinatology Research Branch (NIH/NICHD)
Street address 3990 John R
City Detroit
State/province MI
ZIP/Postal code 48188
Country USA
 
Platform ID GPL7723
Series (1)
GSE27441 Amniotic microRNA profile of normal delivery at term

Data table header descriptions
ID_REF
VALUE background corrected lowess normalized log2 ratio (test/common reference)

Data table
ID_REF VALUE
1100 -0.597013805
3320 -0.221376337
3980 -0.207717048
4040 0.541766075
4390 1.542168025
4610 -0.493805529
4700 -0.426622947
5250 0.260248176
5560 1.191359322
5730 -0.315967125
5740 -0.769556098
6880 0.513465565
9578 -0.389618488
9938 0.036255828
10138 0.051529536
10306 0.039269524
10482 0.78413103
10618 0.396259061
10899 -0.273522171
10901 0.285076634

Total number of rows: 1986

Table truncated, full table size 35 Kbytes.




Supplementary file Size Download File type/resource
GSM678292_ch1_1_Exiqon_14069148_S01_Cropped.txt.gz 828.8 Kb (ftp)(http) TXT
GSM678292_ch2_0_Exiqon_14069148_S01_Cropped.txt.gz 823.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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