Sus scrofa breed:Anqing Six-end-white pig
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PROVIDER: PRJNA1244269 | ENA |
REPOSITORIES: ENA
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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:We sequenced the whole mRNA of six pig (Sus scrofa) fat, liver and muscle tissues, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising. whole mRNA sequencing profiles of six pig (Sus scrofa) fat, liver and muscle tissues
2014-09-01 | E-GEOD-45204 | 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). 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:Sus scrofa breed:Large White | cultivar:pig Transcriptome or Gene expression
| PRJNA293404 | ENA
Project description:Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from 7 RNA follicle pools and several technical replicates were made. Four Large, one Medium and two Small follicles pools were considered. For each follicle pool, 2 radioactive labellings were performed. Each membrane was exposed 16 hours (to avoid saturation of the signal of highly expressed genes) and 28 hours (to get some signal from lowly expressed genes). Each probe was hybridised on GPL3971 scag_scai Sus scrofa 1.2K mono array and on GPL3970 scag_scai Sus scrofa 4.6K triplicate array (except for GFS2172 which was labelled only once and hybridised onto 2 GPL3971 scag_scai Sus scrofa 1.2K mono array membranes), so that 4 spots are available for each gene (and 2 spots for GFS2172), for a given RNA and a given radioactive labelling. Keywords: granulosa-cell transcriptome analysis data consisted in (6 RNA x 2 labellings) + (GFS2172 RNA X 1 labelling)= 13 probes, 26 hybridisations, 52 images.
2010-06-30 | E-GEOD-5299 | biostudies-arrayexpress
Project description:Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from 7 RNA follicle pools and several technical replicates were made. Four Large, one Medium and two Small follicles pools were considered. For each follicle pool, 2 radioactive labellings were performed. Each membrane was exposed 16 hours (to avoid saturation of the signal of highly expressed genes) and 28 hours (to get some signal from lowly expressed genes). Each probe was hybridised on GPL3971 scag_scai Sus scrofa 1.2K mono array and on GPL3970 scag_scai Sus scrofa 4.6K triplicate array (except for GFS2172 which was labelled only once and hybridised onto 2 GPL3971 scag_scai Sus scrofa 1.2K mono array membranes), so that 4 spots are available for each gene (and 2 spots for GFS2172), for a given RNA and a given radioactive labelling. Keywords: granulosa-cell transcriptome analysis
2008-06-12 | GSE5299 | GEO
Project description:Cilia from two fresh pig tracheas (Sus scrofa) were removed by calcium shock and proteins extracted in buffer containing 1% NP40. Extract was diluted to reduce salts and fractionated by HPLC on a mixed bed ion exchange column. Fractions were reduced/alkylated and digested with trypsin for analysis by LC-MS/MS on an orbitrap fusion Lumos using a 75 minute top speed DDA method and HCD.
2023-05-04 | MSV000091856 | MassIVE
Project description:Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. After a strict CNV calling pipeline it was identified 40 copy number variable regions covering all the four chromosomes, with some overlapping segmental duplications and pig unigenes. This CNV snapshot analysis lays the groundwork for a better understanding of porcine phenotypes and genotypes for the identification of important economic traits. Keywords: comparative genome hybridization, CNV, Sus Scrofa, Nimblegen tiling array A custom 385k tiling-path array CGH was designed (Nimblegen Systems) to cover the preliminary Sus Scrofa assembly for chromosomes 4, 7, 14 and 17, from the August 2007 release (http://www.sanger.ac.uk/Projects/S_scrofa/), which was the newest version at the time of the experiment. From a pig family-material comprising 14 boar founders, 700 sows and about 12.000 offspring, 12 Duroc boar founders (A, B, C, D, E, G, H, J, K, L, M and N) were selected to function as test animals. An unrelated boar of the Hampshire breed was selected as the common reference. Each of the 12 boars were hybridized twice (technical replicates, 24 arrays) against the common reference.
2010-06-21 | E-GEOD-10753 | biostudies-arrayexpress
Project description:Proteins are essential for sperm function, including fertilizing capacity. Pig spermatozoa, emitted in well-defined ejaculate fractions, clearly vary in their functionality, which would be related to differences in protein composition. This study aimed firstly to update the porcine sperm proteome and secondly to identify proteins differentially expressed among mature spermatozoa from cauda epididymis and those fortuitously delivered in different ejaculate portions. Nine ejaculates from nine mature and fertile boars were manually collected in three separate ejaculate portions: the first 10 mL of sperm-rich ejaculate fraction (SRF), the rest of SRF and the post-SRF. The contents of cauda epididymides of the same boars was collected post-mortem by perfusion. All samples were centrifuged, pooling the resulting sperm pellets within the respective source-sample, which were later split to generate two technical replicates per source. The final eight sperm samples were subjected to iTRAQ-based 2D-LC-MS/MS for protein identification and quantification. A total of 1,723 proteins were identified (974 of Sus Scrofa taxonomy) and 1,602 of them were also quantified (960 of Sus Scrofa taxonomy). After an ANOVA test, 32 Sus Scrofa proteins showed quantitative differences (P < 0.01) among the sperm samples, which were particularly relevant for the functionality of spermatozoa fortuitously ejaculated in the post-SRF. The present study is the first showing quantitative differences in the protein profile of mature spermatozoa, involving proteins clearly implicated in sperm function, that prove the protein profile of boar spermatozoa is remodelled during ejaculation . These findings provide a valuable groundwork for further studies focused on identifying protein biomarkers of sperm fertility.
2018-10-02 | PXD010062 | Pride