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Sample GSM1054014 Query DataSets for GSM1054014
Status Public on Apr 15, 2014
Title Oocyte_prepubertal_rep3
Sample type RNA
Source name Oocyte, prepubertal B6C3F1 mice, 3 weeks of age, replicate 3
Organism Mus musculus
Characteristics strain: B6C3F1
cell type: oocyte
age: 3 weeks of age
developmental stage: prepubertal
Treatment protocol Mice were injected with 10 IU PMSG and 10 IU hCG i.p. 48 hours apart, and sacrificed by cervical dislocation 14 h after hCG injection. Metaphase II oocytes were retrieved from the oviductal ampullae, and freed of cumulus cells and zonae pellucidae, before lysing in SDS lysis buffer (4% SDS, 100 mM Tris/HCl pH 7.5, 0.1 M DTT, total volume 70 µL).
Growth protocol B6C3F1 mice (C57Bl/6J · C3H/HeN) aged 3, 8 and 52 weeks (prepubertal, mid-age, climacteric) were maintained and used for experiments according to the ethical permit issued by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV) of the state of North Rhine-Westphalia, Germany. Throughout the extended time of this study, mice were reared, housed, fed ad libitum and primed for superovulation.
Extracted molecule total RNA
Extraction protocol RNA (samples in 300 μL RLT buffer with 1% β-mercapt- oethanol) was isolated using RNeasy Micro Kit as described by the manufacturer (Qiagen, no DNase treatment). An examina- tion of total RNA on an Agilent 2100 Bioanalyzer and RNA Pico 6000 Lab-Chip kit confirmed the extraction of high-quality RNA, which was then prepared for gene expression profiling. Arcturus RiboAmp HS Plus Amplification Kit (MDS Analytical Technologies GmbH, Germany) was used to amplify total RNA (two rounds of amplification) according to manufacturer’s instructions. After the second round of amplification, ampli- fied RNA was eluted with 15 μL RE buffer. Concentration of amplified RNA was measured using Agilent Bioanalyzer 2100 and RNA 6000 Lab-Chip kit.
Label Cy3
Label protocol Three micrograms of amplified RNA were labeled with Cy3 using Arcturus Turbo Labeling CY3 Kit (MDS Analytical Technologies GmbH, Germany). Concentration and frequency of incorporation (FOI) were measured using the NanoPhotometer (Implen, Munich, Germany).
Hybridization protocol Fragmentation (1650 ng Cy3-labeled amplified RNA) and hybridization were performed following the hybridization pro- cedure recommended by the array manufacturer (Agilent Tech- nologies), with a modification given by the manufacturer of the Turbo Labeling CY3 Kit.
Scan protocol Microarray wash and detection of the labeled RNA on GeneChips were performed according to the instructions of Agilent Technologies. Gene expression profiling was performed using Agilent’s Whole Mouse Genome Oligo Microarrays (4 44k, each array with 41 174 features).
Description Gene expression of prepubertal mouse oocyte
Data processing Array image acquisition and feature extraction was performed using the Agilent G2505B Microarray Scanner and Feature Extraction software version 9.5 (Agilent Technologies).
Submission date Dec 17, 2012
Last update date Apr 15, 2014
Contact name Marcin Siatkowski
Phone 0048668859148
Organization name IBIMA
Street address Ernst-Heydemann-Str. 8
City Rostock
ZIP/Postal code 18059
Country Germany
Platform ID GPL11202
Series (1)
GSE42959 Maternal age effect on mouse oocytes: new biological insight from proteomic analysis

Data table header descriptions
VALUE Quantile normalized signal intensity

Data table
GE_BrightCorner 15.12664282
DarkCorner 6.852930097
A_55_P1989846 6.8020443
A_55_P1991598 6.698239596
A_55_P2022211 12.42720303
A_55_P1980764 8.435006503
A_55_P1964375 10.66618445
A_51_P128876 14.458576
A_55_P2121042 7.557726794
A_52_P219230 7.003304768
A_51_P207591 7.348336203
A_55_P2131920 7.236956966
A_55_P2404223 8.557196646
A_55_P2101944 14.74052315
A_52_P358860 7.268088854
A_51_P119031 14.07179622
A_51_P309854 13.65061409
A_51_P343900 14.69123044
A_51_P234359 7.802934986
A_51_P487813 8.478502107

Total number of rows: 39485

Table truncated, full table size 983 Kbytes.

Supplementary file Size Download File type/resource
GSM1054014_Prepubertal_rep3.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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