Transcriptome sequencing of porcine liver samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: Angel Mario Montes
PROVIDER: E-GEOD-75850 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptome analysis of a population of control animals and RNAi-treated to partially inactivate genes that are homologs to human genes causing Retinitis Pigmentosa. RNA-seq analyses were performed at L3 larval stage in wild type, and smg-1(r861) mutants that have a defective Non-mediated decay pathway. RNA-seq experiments were also performed in adults glp-4(bn2) mutants that lack of germline. synchronized N2 and smg-1(r861) L1 larvae fed for 24 hours at 20 °C with the RNAi clones of prp-6, prp-8, prp-31 and gfp; and 5-day adult glp-4(bn2) worms grown at 25 °C and fed first, for 72 hours with OP50 and next, for 48 more hours with the RNAi clones of prp-8, prp-31 and gfp
2016-07-03 | E-GEOD-72952 | biostudies-arrayexpress
Project description:Purpose: Identification of genes regulating growth and fatness traits in pig. Methods: Hypothalamic transcriptome analysis through RNA-seq and differential expression analysis of divergent pigs for growth and fatness traits. Results: Characterization of the transcripts expressed in the porcine hypothalamus and identification of differentially expressed genes, some of them located within previously described QTL regions. Conclusions: Characterization of porcine hypothalamic transcriptome and identification of relevant genes and transcription factors related to the traits of interest. Transcriptome sequencing of 10 hypothamic samples of two groups of divergent pigs for growth and fatness (five per group).
2013-11-01 | E-GEOD-51968 | biostudies-arrayexpress
Project description:The knowledge of the genetic architecture behind feed efficiency would allow to breed more efficient animals maximizing farm profitability and reducing the environmental impact of animal production. This study analyzes high throughput gene expression data from milk samples to determine key genes and biological mechanisms associated to feed efficiency in dairy sheep.A detailed description of the sheep management practices and calculations for the feed efficiency index (FEI) are detailed in 10.3168/jds.2020-19061. For these analyses, we selected animals with divergent FEI values from a group of 40 lactating Assaf ewes. RNA-Seq was performed on milk somatic cell samples from 8 high feed efficiency sheep (H-FE), FEI = −0.29 (SD = 0.23), RFI = −0.16 (SD = 0.25), and 8 low feed efficiency sheep (L-FE), FEI = 0.81 (SD = 0.24), RFI = 0.19 (SD = 0.24)).
2023-02-14 | E-MTAB-12355 | biostudies-arrayexpress
Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels. Liver mRNA profiles of intact male pigs fed a HFC diet, castrated male pigs fed a HFC diet, and castrated male pigs treated with testosterone fed a HFC diet were generated by deep sequencing, using Illumina HiSeq 2000.
2015-01-08 | E-GEOD-62696 | biostudies-arrayexpress
Project description:Sma- and Mad-related protein 4 (SMAD4) is closely associated with the development of ovarian follicular. However, current knowledge of the genome-wide view on the role of SMAD4 gene in mammalian follicular granulosa cells (GCs) is still largely unknown. In the present study, RNA-Seq was performed to investigate the effects of SMAD4 knockdown by RNA interference (SMAD4-siRNA) in porcine follicular GCs. A total of 1025 differentially expressed genes (DEGs), including 530 upregulated genes and 495 downregulated genes, were identified in SMAD4-siRNA treated GCs compared with that treated with NC-siRNA. Furthermore, functional enrichment analysis indicated that upregulated DEGs in SMAD4-siRNA treated cells were mainly enriched in cell-cycle related processes, interferon signaling pathway, and immune system process, while downregulated DEGs were mainly involved in extracellular matrix organization/disassembly, pathogenesis, and cell adhesion. In particular, cell cycle and TGF-β signaling pathway were discovered as the canonical pathways changed under the SMAD4 silencing. Taken together, our data reveals SMAD4 knockdown alters the expression of numerous genes involved in key biological processes of the development of follicular GCs and provides a novel global clue of the role of SMAD4 gene in porcine follicular GCs. mRNA profiles of NC-siRNA treated and SMAD4-siRNA treated porcine GCs were generated by RNA sequencing using Ion Torren Proton
2016-07-25 | E-GEOD-76833 | biostudies-arrayexpress
Project description:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Bromeliaceae family is an example of a large and well described adaptive radiation of plant families in the Neotropics. This family is composed of terrestrial xerophytes and both facultative and obligatory epiphytes, occurring in a wide range of habitats. Bromeliads have different habits, varying from terrestrial to epiphytical, and are found from sea level to altitudes above 4,000 m, in both desert and humid regions, as well as in soils subject to regular floods and in places with very little or great luminosity. This huge habitat plasticity makes bromeliads an interesting model to study the expression of miRNAs in different natural conditions and the first step is to identify miRNAs and its targets. For this purpose, we used a high-throughput sequencing analysis (Solexa technology) of small RNAs (sRNAs) from the endemic South American species Vriesea carinata. RNA profiles in 1 leaf library of Vriesea carinata by deep sequencing (Illumina HiSeq2000)
2014-04-25 | E-GEOD-38248 | biostudies-arrayexpress
Project description:Dietary supplementation with fish-oil modulates ruminant milk composition towards a healthier fatty acid profile for consumers, but it also causes milk fat depression (MFD). Because the dairy goat industry is mainly oriented towards cheese manufacturing, MFD can elicit economic losses. There is large individual variation in animal susceptibility with goats more (RESPO+) or less (RESPO−) responsive to diet-induced MFD. Thus, we used RNA-Seq to examine gene expression profiles in mammary cells to elucidate mechanisms underlying MFD in goats and individual variation in the extent of diet-induced MFD.
2022-12-11 | E-MTAB-11581 | biostudies-arrayexpress
Project description:Recently, microRNAs (miRNAs), known to modulate gene expression through post-transcriptional mechanisms, were implied in regulation of early pregnancy events including maternal recognition of pregnancy and implantation. To characterize complex transcriptomic changes in expression of miRNAs in pregnant and cyclic endometria collected on days 12, 16 and 20 was analyzed using Illumina deep sequencing. This research showed repertoire of pregnancy-related miRNAs in porcine endometrium during initial stages of conceptus implantation and during the estrous cycle and sheds light on miRNA-mediated gene expression regulation mechanism at the maternal-conceptus interface. miRNAs and isomiRs expression profiles were analyzed in samples collected from porcine endometrium on Days 12, 16 and 20 of pregnancy and estrous cycle. Each group was represented by 4 to 6 samples. Generated libraries were run in multiplex using specific barcodes to differentiate samples. Illumina sequencing was performed in duplicate (two runs) and after demultiplexing, the same samples from two independent runs were concatenated.
2015-11-06 | E-GEOD-64863 | biostudies-arrayexpress
Project description:In order to understand the complexity of gene regulation downstream of IIS, we did RNA-seq in mixed culture in wild-type, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20 and correlated it with ChIP-seq data RNA-seq profile of different mutants in mix stage
2016-03-01 | E-GEOD-67975 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-01-07 | E-GEOD-38212 | biostudies-arrayexpress