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Sample GSM897395 Query DataSets for GSM897395
Status Public on Oct 14, 2012
Title OM_PV_T31
Sample type RNA
 
Source name rainbow trout ovarian follicles, post-vitellogenesis, prophase I, highly responsive to hormone stimulation, sample 31
Organism Oncorhynchus mykiss
Characteristics tissue: ovarian follicles
stage of oogenesis: post-vitellogenesis
meiotic stage: prophase I
development capacity: developmentally competent
Treatment protocol Individual follicles were isolated and the follicular layers dissected out using forceps in trout mineral medium.
Growth protocol Samples were collected from 3-year old rainbow trout females during reproductive season during late-vitellogenesis (NC1 samples), post-vitellogenesis (C1 samples) and after meiosis resumption (C2 samples).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.35 µg RNA using the One-Color Microarray based gene Expression kit (Quick Amp Labeling, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2566AA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in rainbow trout follicles in which prophase I oocytes are meiotically competent and developmentally competent after meiosis resumption
Data processing The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities. Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 3 out of 4 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation
 
Submission date Mar 19, 2012
Last update date Oct 14, 2012
Contact name Julien Bobe
E-mail(s) Julien.Bobe@rennes.inra.fr
Phone (33) 2 23 48 57 24
Organization name Institut National de la Recherche Agronomique
Lab INRA-SCRIBE
Street address Campus de Beaulieu
City Rennes
ZIP/Postal code 35000
Country France
 
Platform ID GPL15258
Series (2)
GSE36602 Transcriptional profiling of somatic cells differentiation throughout oocyte competence acquisition in rainbow trout ovarian follicles.
GSE36617 Contribution of molecular actors from somatic origin to oocyte developmental competence acquisition, lessons from evolution

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (log2 values) calculated by Genespring Agilent GX10.0 software

Data table
ID_REF VALUE
GE_BrightCorner 11.321126
TC105803 12.88655
TC123150 4.8658886
TC109495 12.882461
TC99566 4.325807
TC117962 6.74307
TC109522 11.980259
TC105316 10.209999
TC105523 12.833952
TC109757 8.21951
TC97672 13.501085
TC97554 6.699023
TC112134 11.562694
TC129300 3.4162452
TC119203 5.221536
TC120707 9.717522
TC118684 4.770447
TC115043 11.102462
TC103235 4.6425567
TC130279 11.955937

Total number of rows: 26666

Table truncated, full table size 477 Kbytes.




Supplementary file Size Download File type/resource
GSM897395_OM_PV_T31.txt.gz 7.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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