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Sample GSM644058 Query DataSets for GSM644058
Status Public on Jun 30, 2011
Title Mus Musculus_wild-type fully-grown oocyte_rep2
Sample type RNA
 
Source name Mus musculus oocyte wild-type
Organism Mus musculus
Characteristics gender: Female
age: 8-12 weeks-old mice
cell type: Oocyte
developmental stage: Fully-grown, GV germinal vesicule stage
genetic background: wild-type
genotype: mixed 129XI/SvJ and C57BL/6
Growth protocol Fully grown oocytes (GV) were collected from ovaries of 8-12 week-old mice (WT, Hsf1 mutant or Hsf2 mutant) in M2 medium (SIGMA).
Extracted molecule total RNA
Extraction protocol Total RNA from 200 to 400 fully grown oocytes (GV) from each genotype (WT, Hsf1 mutant or Hsf2 mutant) were extracted using Qiagen RNeasy micro kit and 10ng samples of RNA were amplified using NuGen WT ovation Pico RNA amplification system to obtain about 10µg of single-strand (ss) cDNA. Two micrograms of ss cDNA was converted to double-strand cDNA using Klenow fragment of the DNA polymerase I and the synthesized cDNAs were then incubated with 1μl of 4 mg/ml RNase A at 37 °C for 10 minutes, precipitated and the pellet dissolved with 20μl of nuclease-free water.
Label Cy5
Label protocol The cDNA of each sample (3.5μg) was synthesized as probe and labeled with Cy3- or Cy5-conjugated random nonamers (TriLink Biotechnologies, San Diego, CA).
 
Hybridization protocol Labelled cDNA were hybridized to a NimbleGen Mus musculus Gene Expression 385K microarray, containing 42,586 probe sets with up to 9 probes of 60mer oligonucleotides per gene, following the protocol by Roche NimbleGen, Inc. (Madison, USA). The microarrays were incubated on the NimbleGen Hybridization System 4 (Roche NimbleGen) for 16 hours at 42 °C. The hybridized slides were washed at 10× wash buffer I, II and III (Roche NimbleGen) and dried by nitrogen gas at room temperature.
Scan protocol Slides were scanned with an Axon GenePix Pro 4200A microarray scanner at 5μm resolution, 532 nm and 635nm wavelengths software using associated software GenePix Pro software (Molecular Devices, Sunnyvale, CA). The scanned images of the arrays were quantified using NimbleScan software (Roche NimbleGen).
Description This sample is of wild-type oocytes. It is the second of two wild-type technical replicates used in this experiment.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Dec 21, 2010
Last update date Jun 30, 2011
Contact name Florent LE MASSON
E-mail(s) lemasson@cict.fr
Phone 0561557750
Organization name CNRS
Lab Centre de Biologie du Développement
Street address 118 route de Narbonne Bat4R3b3
City Toulouse
ZIP/Postal code 31062
Country France
 
Platform ID GPL7437
Series (1)
GSE26240 Expression analysis of fully-grown oocyte collected from mouse wild-type, Hsf1 mutant or Hsf2 mutant

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged log2 signal intensity

Data table
ID_REF VALUE
AB001539 9.01308
AB001926 12.77984
AB003147 6.63027
AB003503 13.69791
AB004048 7.4232
AB005654 9.90377
AB005662 7.62861
AB006034 6.12703
AB006329 6.75926
AB007811 6.59556
AB008175 7.12878
AB008937 6.39982
AB009688 6.25093
AB011370 7.40909
AB011499 10.93575
AB011812 10.47698
AB012265 9.60334
AB012601 11.88524
AB012808 7.6153
AB013097 6.48168

Total number of rows: 42586

Table truncated, full table size 745 Kbytes.




Supplementary file Size Download File type/resource
GSM644058.pair.gz 6.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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