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Sample GSM572675 Query DataSets for GSM572675
Status Public on Dec 31, 2012
Title Bt-2319-180-55-0308-7j
Sample type RNA
 
Source name Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 7759
Organism Bos taurus
Characteristics annotation pf/mf/gf: PF
group: small follicles
date hybridation-genovul: 2008-03-25
status: S (healthy follicles)
animal-number_genovul: 7759
Extracted molecule total RNA
Extraction protocol Once ovaries collected, all visible antral follicles larger than 1 mm in diameter for sows and 3 mm for cows were isolated carefully using a binocular microscope. After dissection, follicle diameter was measured and each follicle was classified according to size, animal and follicular quality. Follicles were allocated to two size classes: small (noted SF, 1-2 mm for sows and 3-5mm for cows) and large (noted LF, 7-8 mm for sows and 15-20mm for cows). Granulosa cells were recovered from all individual follicles and they were stored at -80°C until RNA extraction. For each follicle, a sample of granulosa cells was smeared on a histological slide, and then Feulgen stained to determine follicular quality by microscopic examination. Only healthy follicles (presence of mitosis and absence of pycnosis in granulosa cells) were kept for this study. RNA was extracted from granulosa cells according to the technique described by Chomczynski and Sacchi with minor modifications using pools of granulosa cells from the same follicle size class and the same animal. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies, Massy, France) and low-quality RNA preparations were discarded.
Label P33
Label protocol The arrays were hybridized with 33P-labelled complex probes synthesized from 5 µg of each RNA sample, using SuperScript II RNAse H-reverse transcriptase (Invitrogen, Cergy-Pontoise, France)
 
Hybridization protocol Micro-arrays were first hybridized with a 33P-labelled oligonucleotide sequence present in all PCR products to control the quality of the spotting process and to evaluate the amount of DNA in each spot. After stripping, the arrays were hybridized with 33P-labelled complex probes synthesized from 5 µg of each RNA sample, using SuperScript II RNAse H-reverse transcriptase (Invitrogen, Cergy-Pontoise, France). Each complex probe has been hybridized on membrane exposed 1, 3 or 7 days to radioisotopic-sensitive imaging plates (BAS-2025, Fujifilm, Raytest, Courbevoie, France).
Scan protocol The imaging plates were scanned thereafter with a phosphor imaging system at 25µm resolution (BAS-5000, Fujifilm, Raytest, Courbevoie, France). Hybridization images obtained from oligonucleotide and complex probes were quantified using the semi-automated AGScan software.
Description A pig nylon micro-array is hybridized with a complex 33P labelled probe
Data processing Data exploration and analysis were performed using R software. The data coming from complex probes hybridization were analysed on the logarithmic scale. As a first step, negative spot with >7 intensity values were checked on images and replaced by the median of negative spots in case of obvious overshining effect or hybridization stain. Then, luciferase positive controls were removed and the correlations of the data from each membrane were examined intra condition. Hybridizations with a lower than 0.80 correlation coefficient were discarded. Spots with low signal value (below the average of empty spots + 3 standard deviations) were considered as unexpressed and were excluded from the analysis. Finally, the negative control spots were removed and the remaining data were centred for each membrane.
 
Submission date Jul 30, 2010
Last update date Dec 31, 2012
Contact name Gwenola Tosser-Klopp
E-mail(s) gwenola.tosser@toulouse.inra.fr
Phone 33 5 61 28 51 14
Organization name INRA
Lab Genetique Cellulaire
Street address Chemin de Borde-Rouge BP 52627
City Castanet-Tolosan Cedex
ZIP/Postal code 31326
Country France
 
Platform ID GPL3729
Series (2)
GSE23335 SABRE-Bt-Ssc_020410
GSE24221 Genovul-Bt-Ssc_020410

Data table header descriptions
ID_REF
VALUE see data processing protocol
QIM_CONST image signal intensity constant diameter
QFIT_VAR fit signal intensity varariable diameter
FIT_CORR fot correction
QIM_VAR image signal intensity variable diameter
QFIT_CONST fit signal intensity constant diameter
DIAM variable diameter
SPOT_QUAL spot quality
OVER_CORR overshining correction
QM quality measure

Data table
ID_REF VALUE QIM_CONST QFIT_VAR FIT_CORR QIM_VAR QFIT_CONST DIAM SPOT_QUAL OVER_CORR QM
scaa0084.b.16 2.100315898 1307 1438 -0.01065 1443 1300 320.678 1 0 0.86745
scan0036.n.13 null 177 225 0.00502 223 176 350 0 0 0.88535
scan0030.h.24 null 135 145 0 179 115 350 0 0 0.82704
scan0024.i.24 null 143 188 0.00488 189 144 350 0 0 0.87557
scan0018.j.05 null 144 143 0 192 115 350 0 0 0.80773
scan0012.e.22 0.252702354 206 261 0.00468 261 204 350 0 0 0.84612
scan0006.g.20 -0.025317808 156 87 0 221 71 350 0 0 0.56144
scaj0003.d.22 -0.223143551 128 108 0 173 87 350 0 0 0.74287
scac0041.n.16 -0.155192889 137 106 0 185 86 350 0 0 0.71518
scac0033.p.18 0.155934802 187 132 0.00552 131 189 239.465 0 0 0.86297
scac0029.i.16 -0.25489225 124 194 0 163 156 350 0 0 0.8394
scac0025.g.19 null 115 74 0 152 60 350 0 0 0.64761
scaa0084.l.24 null 139 99 0 194 81 350 0 0 0.65656
scan0036.n.16 null 141 29 0.0065 28 145 119.578 0 0 0.84619
scan0030.i.03 null 113 152 0 148 121 350 0 0 0.85019
scan0024.j.08 null 131 130 0 175 104 350 0 0 0.80371
scan0018.j.07 0.345361184 226 288 0.00298 289 230 350 0 0 0.84796
scan0012.f.05 0.100975917 177 92 0 240 74 350 0 0 0.55202
scan0006.g.24 -0.14792013 138 110 0 192 90 350 0 0 0.69243
scaj0003.i.23 -0.091567194 146 166 0 190 132 350 0 0 0.83994

Total number of rows: 9216

Table truncated, full table size 537 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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