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Sample GSM132660 Query DataSets for GSM132660
Status Public on Sep 05, 2006
Title Mature MII-oocyte sample #2
Sample type RNA
 
Source name oocyte
Organism Mus musculus
Characteristics Mature MII-oocyte isolated eCG944-46h)/hCG(14h)-treated female 22-24 days old (C57BL/6JxSJL)F1 mice
Biomaterial provider The Jackson Laboratory
Treatment protocol Ovarian follicular development was stimulated by intraperitoneal injection of 5 IU of eCG (EMD Biosciences, Inc., Calbiochem, La Jolla, CA). Mice were then injected with hCG (5IU/mouse), and the oviducts were removed 14 h post hCG injection. Ovulated OCCs were released by gently teasing apart the ampulla of oviducts. Denuded oocytes were obtained by incubating the mass of OCCs in medium containing 1 mg/ml of hyaluronidase for about 3-5 min at 37 ?C. Mature oocytes with a visible first polar body (hereafter termed MII oocytes) and no apparent sign of degeneration were collected. Both GV and MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present.
Growth protocol MII oocytes were washed thoroughly in the collection medium to ensure that no cumulus cells were present. Medium used for oocyte collection was the same as for collection of GV-oocytes
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 300 oocytes using the Picopure RNA isolation Kit (Arcturus, Mountain View, CA).
Label Biotin
Label protocol Total RNA was extracted from oocytes using the PicoPure RNA Isolation Kit according to the manufacturer?s instruction. The RNA quality and yield of each sample were determined using the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) in combination with Quant-iTTM RiboGreen Reagent according to supplied protocols (Invitrogen, Carlsbad, CA). Ten nanograms of total RNA from each sample was employed in the two-round cDNA synthesis and subsequent in vitro-transcription according to the Two-Cycle Eukaryotic Target Labeling Assay (Affymetrix Expression Analysis Technical Manual: ? Section 2: Eukaryotic Sample and Array Processing? (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)) with the following modifications. For the first and second cycle of cDNA synthesis steps, Full Spectrum? MultiStart Primers for in vitro transcription (SystemBiosciences, Mountain View, CA) were used, instead of Affymetrix?s standard T7-Oligo(dT) primer or random hexamers.
 
Hybridization protocol Standard AffyMetrix procedures
Scan protocol Standard AffyMetrix
Description Mature MII-stage oocytes isolated from 22-24d old eCG(44-46h)/hCG(14h)- treated mice.
Data processing Probe level data were imported into the R software environment and expression values were summarized using the RMA (Robust MultiChip Average) function (Irizarry et al., 2003) in the R/affy package with rma2 background adjustment, no inter-array normalization, and median polish summarization of perfect match values (Gautier et al., 2004). To account for the difference in starting RNA amount obtained from the same number of GV and MII oocytes, and based on the fact that there is no new transcriptional activity in the fully grown oocytes (De La Fuente, 2006), a normalization was performed on a sample of non-differentially expressed genes which were estimated and sampled using EM algorithm for a normal mixture model (Gautier et al., 2004; McLachlan and Krishnan, 1997)
 
Submission date Aug 29, 2006
Last update date Aug 28, 2018
Contact name You-Qiang Su
E-mail(s) youqiang.su@jax.org
Organization name The Jackson Laboratory
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL1261
Series (1)
GSE5668 Identification and characterization of the changed and stable transcripts during mouse oocyte maturation
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
1415670_at 6.719676654
1415671_at 7.261820325
1415672_at 10.26865808
1415673_at 4.733324147
1415674_a_at 5.039642465
1415675_at 5.836841125
1415676_a_at 4.67414048
1415677_at 8.485627642
1415678_at 9.786572458
1415679_at 10.17209995
1415680_at 8.865270851
1415681_at 3.04882617
1415682_at 7.762948348
1415683_at 7.852756804
1415684_at 9.026802171
1415685_at 4.149021772
1415686_at 9.391554817
1415687_a_at 6.996990915
1415688_at 7.529567691
1415689_s_at 2.652829732

Total number of rows: 21702

Table truncated, full table size 497 Kbytes.




Supplementary file Size Download File type/resource
GSM132660.CEL.gz 5.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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