SABRE-Bt-Ssc_020410
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa Bos taurus
PROVIDER: GSE23335 | GEO | 2012/12/31
SECONDARY ACCESSION(S): PRJNA131217
REPOSITORIES: GEO
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Project description:In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. In this project, we proposed to study the genetic determinism that underlies the difference of ovulation rate between species (cattle and pigs), by studying two processes that exist in ovary: follicular development and follicular atresia. Towards this purpose, we made a comparative transcriptomics study on granulosa cells. Pig and cattle comparison was achieved by a transcriptome analysis with a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF), small atretic follicles (SAF) or large healthy antral follicles (LHF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis on pig and cattle evidenced 997 differentially expressed genes (FDR1%) between the three follicle classes and/or the two species. This research project which implicated three laboratories from INRA: "Laboratoire de Genetique Cellulaire" (UMR444-LGC) , "Station d'Amelioration Genetique des Animaux" (UR 631-SAGA) and "Physiologie des Comportements et de la reproduction" (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through GenOvul project. Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray
2012-12-31 | GSE24221 | GEO
Project description:In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. In this project, we proposed to study the genetic determinism that underlies the difference of ovulation rate between species (cattle and pigs), by studying two processes that exist in ovary: follicular development and follicular atresia. Towards this purpose, we made a comparative transcriptomics study on granulosa cells. Pig and cattle comparison was achieved by a transcriptome analysis with a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF), small atretic follicles (SAF) or large healthy antral follicles (LHF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis on pig and cattle evidenced 997 differentially expressed genes (FDR1%) between the three follicle classes and/or the two species. This research project which implicated three laboratories from INRA: "Laboratoire de Genetique Cellulaire" (UMR444-LGC) , "Station d'Amelioration Genetique des Animaux" (UR 631-SAGA) and "Physiologie des Comportements et de la reproduction" (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through GenOvul project. Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray The data were obtained from 34 RNA samples: 10 small healthy follicles samples (6 for sows and 4 for cows), 13 small atretic follicles samples (7 for sows and 6 for cows) and 11 samples for large healthy follicles (6 for sows and 5 for cows). They were hybridized on a 9K pig nylon microarray (GPL3729).
2012-12-31 | E-GEOD-24221 | biostudies-arrayexpress
Project description:In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. In this project, we proposed to study the genetic determinism that underlies the difference of ovulation rate between species (cattle and pigs). Towards this purpose, we made a comparative transcriptomics study on granulosa cells. Pig and cattle comparison was achieved by a transcriptome analysis with a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF) or large healthy antral follicles (LHF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis on pig and cattle evidenced 252 differentially expressed genes (FDR5%) between the two follicle classes and/or the two species. This research project which implicated three laboratories from INRA: M-BM-+ Laboratoire de GM-CM-)nM-CM-)tique Cellulaire M-BM-; (UMR444-LGC) , M-BM-+ Station dM-bM-^@M-^YAmM-CM-)lioration GM-CM-)nM-CM-)tique des Animaux M-BM-; (UR 631-SAGA) and M-BM-+ Physiologie des Comportements et de la reproduction M-BM-; (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through GenOvul project. Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray The data were obtained from 21 RNA samples: 10 small healthy follicles samples (6 for sows and 4 for cows) and 11 samples for large healthy follicles (6 for sows and 5 for cows). They were hybridized on a 9K pig nylon microarray (GPL3729).
2012-12-31 | E-GEOD-23335 | biostudies-arrayexpress
Project description:In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. Atresia is a phenomenon which affects the majority of developing follicles. In this project, we proposed to study the gene regulation of small antral follicles that are either healthy or undergoing atresia in pigs). Towards this purpose, we made a comparative transcriptomics study on granulosa cells, using a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF) or small antretic follicles (SAF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis evidenced 1682 (912) differentially expressed genes with a 5% (1%) FDR between the two follicle classes. This research project which implicated three laboratories from INRA: "Laboratoire de Genetique Cellulaire" (UMR444-LGC), "Station d'Amelioration Genetique des Animaux" (UR 631-SAGA) and "Physiologie des Comportements et de la reproduction" (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through GenOvul project. Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray The data were obtained from 13 RNA samples: 6 small healthy follicles samples and 7 small atretic follicles. They were hybridized on a 9K pig nylon microarray (GPL3729).
2012-12-31 | E-GEOD-24273 | biostudies-arrayexpress
Project description:In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. Atresia is a phenomenon which affects the majority of developing follicles. In this project, we proposed to study the gene regulation of small antral follicles that are either healthy or undergoing atresia in pigs). Towards this purpose, we made a comparative transcriptomics study on granulosa cells, using a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF) or small antretic follicles (SAF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis evidenced 1682 (912) differentially expressed genes with a 5% (1%) FDR between the two follicle classes. This research project which implicated three laboratories from INRA: "Laboratoire de Genetique Cellulaire" (UMR444-LGC), "Station d'Amelioration Genetique des Animaux" (UR 631-SAGA) and "Physiologie des Comportements et de la reproduction" (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through GenOvul project. Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray
2012-12-31 | GSE24273 | GEO
Project description:Folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration (a process called atresia). Even if atresia involves an apoptosis process, this mechanism is not well understood. The objective of this experiment was : 1) to analyse gene expression in pig granulosa cells of ovarian follicles during atresia using transcriptome analysis with a 9 024 cDNAs microarray, 2) the identification of gene networks involved in pig ovarian follicular atresia. Granulosa cells were isolated from atretic follicles (small, medium or large). Gene expression was analysed by hybridization of nylon cDNA microarrays. The images were quantified using Bzscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Keywords: pig ovary, folliculogenesis, atresia, gene expression, cDNA microarray, bio-analysis
2008-12-31 | GSE7635 | GEO
Project description:Dibutyl phthalate (DBP), di-2-ethylhexyl phthalate (DEHP), and benzyl butyl phthalate (BBP) are three phthalates commonly found in consumer products, including the plastic coating of pharmaceuticals and personal care products. Folliculogenesis, a tightly regulated process occurring in the ovary, is the maturation of an immature primordial follicle to a mature antral follicle. Follicles house the oocyte and antral follicles specifically play a crucial role in ovarian steroidogenesis and ovulation. DBP, BBP, and DEHP have been associated with inhibited antral follicle growth in vitro, decreased ovulation rates in vitro, and decreased antral follicle counts in women. However, little is known about the effects of a three-phthalate mixture on antral follicles in vivo. The objective of this study was to evaluate the effects of a human relevant mixture of DBP, BBP, and DEHP on ovarian follicles through proteome profiling analysis. CD-1 female mice (60 days old) were pipet fed tocopherol stripped corn oil (vehicle control) only or a phthalate mixture (52% DBP, 36% DEHP, and 12% BBP dissolved in vehicle) which modeled human follicular fluid concentrations. The mice were treated with 32µg/kg/day (PHT Mix 32; cumulative estimate in general population) and 500µg/kg/day (PHT Mix 500; cumulative estimate in occupationally exposed individuals) for 10 consecutive days. Proteome profiling of antral follicles (>250µm) was performed via label-free tandem mass spectrometry. A total of 5,417 antral follicle proteins were identified in the three groups, of which 194 were differentially abundant between the vehicle and PHT Mix 32 group, and 136 between the vehicle and PHT Mix 500 group. Gene ontology analysis revealed that the two treatments of the phthalate mixture upregulate and downregulate distinctive processes, supporting non-monotonic effects of phthalates on the antral follicle proteome. Taken together, these results reveal that a human relevant mixture of DBP, BBP, and DEHP alters the antral follicle proteome and merits further evaluation to elucidate the molecular mechanisms by which phthalates cause negative reproductive outcomes.
2024-07-18 | PXD047061 | Pride
Project description:The aim of the study was to describe and characterise the phosphodiesterases in the human ovary. Part of the study included results from analysis of mRNA microarray data from follicles and granulosa cells from three previously published studies(E-MEXP-3783, E-MTAB-2203, E-MTAB-1670). In addition, we used data from two unpublished studies with granulosa cells isolated from 4-6 mm antral follicles and preantral follicles. The included studies covered the folliculogenesis from the preantral stage to after induction of ovulation. For comparison, previously published dataset from heart (E-GEOD-22253, E-MEXP-2654), parietal cortex (E-GEOD-35977), cerebellum (E-GEOD-35974), lung (E-GEOD-43458), and peripheral blood mononucleated cells(E-GEOD-23832) were included in addition to various tissues from Affymetrix's sample data set.
2014-10-31 | E-MTAB-2862 | biostudies-arrayexpress
Project description:Folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration (a process called atresia). Even if atresia involves an apoptosis process, this mechanism is not well understood. The objective of this experiment was : 1) to analyse gene expression in pig granulosa cells of ovarian follicles during atresia using transcriptome analysis with a 9 024 cDNAs microarray, 2) the identification of gene networks involved in pig ovarian follicular atresia. Granulosa cells were isolated from atretic follicles (small, medium or large). Gene expression was analysed by hybridization of nylon cDNA microarrays. The images were quantified using Bzscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Keywords: pig ovary, folliculogenesis, atresia, gene expression, cDNA microarray, bio-analysis Calibrated follicles were isolated from porcine ovaries after ovariectomy (24h ou 96h after the end of progestagen treatment: Regumate 18 days, 20 mg/days). The follicular status was determined by histological criteria using Feulgen coloration (Monget et al. 1993, Besnard et al. 1996). Healthy follicle is characterized by frequent mitosis and pyknosis absence in granulosa cells. Presence of frequent pyknotic bodies in granulosa cells and no mitosis were allocated to atretic cells. Two cross-classified biological factors of pig ovarian follicles are considered : 1) the stage of development of the follicular growth : small (1-2 mm of diameter), medium (3 mm) and large (>5 mm) follicles; 2) the follicular status: healthy (S1) vs beginning (A2) or advanced (A3) atresia. Gene expression was analysed by hybridization of nylon cDNA microarrays (GPL3729). After hybridisation the data analysis using BASE software and statistical analysis was performed to identify regulated genes. For each of three follicle class and three follicle status combination 4 biological replicates were considered. Total 36 membranes were first hybridized with a vector oligonucleotide labeled (T7 probe 5'-taatacgactcactataggga-3') with gamma33P ATP at 42°C during 12h to determine the quality of the spotting process. After being washed, the arrays were exposed 6 or 24 hours to radioisotopic-sensitive imaging plates (BAS-2025, Fujifilm, Raytest France S.A.R.L., Courbevoie, France). The imaging plates were scanned thereafter with a phosphor imaging system at a 25 õm resolution (BAS-5000, Fujifilm, Raytest France S.A.R.L., Courbevoie, France). Data were acquired with help of a microarray image processing software - AGScan (Cathelin, 2006, http://mulcyber.toulouse.inra.fr/projects/agscan/). Fixed circle segmentation, i.e. a grid process with a fixed spot diameter was applied. The hybridization images were quantified by the extraction of the intensity for each spot. Arrays images and data were stored using BASE software (Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, and Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol 3: SOFTWARE0003, 2002) adapted by Sigenae (http://www.sigenae.org) for analysis and storage of radioactitive microarray data
2010-06-24 | E-GEOD-7635 | biostudies-arrayexpress
Project description:Follicles of polycystic ovaries (PCO) often become arrested in early antral stages at around 3 to 11 mm in diameter. The condition disturbs dominant follicle selection and may result in altered ovulation and anovulation. During the growth and development of human follicles, the follicular fluid (FF) constitutes the avascular microenvironment in which the oocyte develops and acts as a vehicle for hormone signaling between cues from circulation and follicular cells. Previous proteomics studies performed on FF from women with polycystic ovarian syndrome (PCOS) have revealed information on the protein changes associated with the pathophysiology of this disorder. However, these studies have been conducted on FF samples obtained in connection with oocyte pick-up during ovarian stimulation right at the time of ovulation and are limited to follicular conditions during the follicular phase of the menstrual cycle. This study aimed to detect proteomic alterations in FF from human small antral follicles (hSAF) obtained from women with PCO as compared to normal women.
2022-04-07 | PXD031485 | Pride