Sus scrofa
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ABSTRACT:
PROVIDER: PRJNA148807 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress. To further investigate the role of miRNAs in different breed-specific metabolic characters, a comparison of miRNA expression profiles in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six LC sciences microarrays containing 236 miRNA procine probes based on miRBase Release 16.0 and 100 custom miRNA probes based on the solex deep sequencing results (li et al.,2010) were used. When compaired with LW piglets, 5 down-regulated and 8 up-regulated miRNAs were detected (fold change >1.2 and p value < 0.1) in the liver of EHL among the 236 miRbase probes. When considering the 100 custom miRNA probes, 2 down-regulated and 5 up-regulated miRNAs were observed. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs. Six newborn male piglets were sampled from three litters (2 from each litter) of purebred EHL and LW sows and sacrificed. Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 M-BM-0C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturerM-bM-^@M-^Ys instructions. Total RNAs of the two littermate piglets were pooled for the microarray analysis. The pooled samples were named as EHL1-3 and LW1-3, representing 3 mixed liver RNA samples each from EHL and LW piglets, respectively. Microarray experiment was performed by a service provider (LC sciences).
2012-06-17 | E-GEOD-33523 | biostudies-arrayexpress
Project description:Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress. To further investigate the role of miRNAs in different breed-specific metabolic characters, a comparison of miRNA expression profiles in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six LC sciences microarrays containing 236 miRNA procine probes based on miRBase Release 16.0 and 100 custom miRNA probes based on the solex deep sequencing results (li et al.,2010) were used. When compaired with LW piglets, 5 down-regulated and 8 up-regulated miRNAs were detected (fold change >1.2 and p value < 0.1) in the liver of EHL among the 236 miRbase probes. When considering the 100 custom miRNA probes, 2 down-regulated and 5 up-regulated miRNAs were observed. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs.
2012-06-18 | GSE33523 | GEO
Project description:Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress.To further investigate the different breed-specific metabolic characters, a comparison of gene expression profile in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six niemblegen 135K expression microarrays were used. Among 44,987 pig transcripts investigated, 23,807 transcripts retained for further analysis after removing the probes with poor quality intensities and low dependability.All these qualified transcripts were then annotated by manual blast and by referring to previously developed protein-based annotation for pigs. In total, we observed 9,447 genes expressed in the liver of new born piglets. The microarray data of LW piglets were treated as control in the selection of differentially expressed genes related to EHL piglets. The FDR (False Discovery Rate) and fold change were calculated by SAMR 3.02. With FDR< 5%, after the removal of redundant and unannotated sequences, 53 genes were found to be significantly up-regulated and 200 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. With FDR < 10%, 298 genes were found to be significantly up-regulated and 510 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs.
2012-06-18 | GSE33524 | GEO
Project description:Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress.To further investigate the different breed-specific metabolic characters, a comparison of gene expression profile in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six niemblegen 135K expression microarrays were used. Among 44,987 pig transcripts investigated, 23,807 transcripts retained for further analysis after removing the probes with poor quality intensities and low dependability.All these qualified transcripts were then annotated by manual blast and by referring to previously developed protein-based annotation for pigs. In total, we observed 9,447 genes expressed in the liver of new born piglets. The microarray data of LW piglets were treated as control in the selection of differentially expressed genes related to EHL piglets. The FDR (False Discovery Rate) and fold change were calculated by SAMR 3.02. With FDR< 5%, after the removal of redundant and unannotated sequences, 53 genes were found to be significantly up-regulated and 200 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. With FDR < 10%, 298 genes were found to be significantly up-regulated and 510 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs. Six newborn male piglets were sampled from three litters (2 from each litter) of purebred EHL and LW sows and sacrificed. Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 M-BM-0C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturerM-bM-^@M-^Ys instructions. Total RNAs of the two littermate piglets were pooled for the microarray analysis. The pooled samples were named as EHL1-3 and LW1-3, representing 3 mixed liver RNA samples each from EHL and LW piglets, respectively. Microarray experiment was performed by a service provider (CapitalBio, Beijing, China). The microarray (Probe length 60-mer, 135K Format) containing 44987 probe sets was provided by Roche-NimbleGen.
2012-06-17 | E-GEOD-33524 | biostudies-arrayexpress
Project description:Comparison between liver transcriptomes of newborn male Erhualian and Large White piglets
| PRJNA148809 | ENA
Project description:The Chinese Erhualian is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Differences in the transcriptome of Chinese Erhualian and Large White ovaries directly result in variation of ovulation rate. To understand the molecular basis related to ovulation rate in Chinese indigenous and Western breeds, samples were collected and used to hybridized. This study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction. Expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Erhualian and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.
2011-12-31 | E-GEOD-23985 | biostudies-arrayexpress
Project description:The Chinese Erhualian is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Differences in the transcriptome of Chinese Erhualian and Large White ovaries directly result in variation of ovulation rate. To understand the molecular basis related to ovulation rate in Chinese indigenous and Western breeds, samples were collected and used to hybridized. This study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.
2011-12-31 | GSE23985 | GEO
Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0). In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).
2013-08-09 | E-GEOD-41488 | biostudies-arrayexpress
Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0).
2013-08-09 | GSE41488 | GEO
Project description:Porcine placenta, Erhualian pigs and Large White pigs, gestation day 75 and 90
| PRJNA105651 | ENA