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Sample GSM1054012 Query DataSets for GSM1054012
Status Public on Apr 15, 2014
Title Oocyte_prepubertal_rep1
Sample type RNA
Source name Oocyte, prepubertal B6C3F1 mice, 3 weeks of age, replicate 1
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 14.95136061
DarkCorner 6.777331497
A_55_P1989846 6.885520731
A_55_P1991598 6.866572425
A_55_P2022211 12.57782331
A_55_P1980764 8.564089181
A_55_P1964375 10.73978942
A_51_P128876 14.76194044
A_55_P2121042 7.572699216
A_52_P219230 6.979424687
A_51_P207591 7.348678785
A_55_P2131920 6.898797059
A_55_P2404223 8.485965948
A_55_P2101944 14.61068704
A_52_P358860 7.40448366
A_51_P119031 13.65638464
A_51_P309854 13.8814456
A_51_P343900 14.01775444
A_51_P234359 7.730892986
A_51_P487813 9.602162798

Total number of rows: 39485

Table truncated, full table size 983 Kbytes.

Supplementary file Size Download File type/resource
GSM1054012_Prepubertal_rep1.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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