Ontology highlight
ABSTRACT:
PROVIDER: PRJNA227748 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome profiling of pig chromosomes regions associated with water holding capacity [PiF1].
| PRJNA227757 | ENA
Project description:Transcriptome profiling of pig chromosomes regions associated with water holding capacity [DuPi]
| PRJNA219166 | ENA
Project description:We also used microarray analysis to examine transcriptomic changes under moderate drought, identifying thousends of genes that potentially mediate moderate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when moderate drought treatment was started by withholding water (defined as day 0 for moderate drought treatment). The relative soil moisture content decreased rapidly and, after about 48 hours the relative soil moisture content was near 50% of the soil water-holding capacity (first moderate drough treated sample M3 were collected at day 3 (72 h after withholding water)). The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened floral bud samples were collected at day 0, 3, 4, 5, 10.
2014-06-01 | E-GEOD-55431 | biostudies-arrayexpress
Project description:We also used microarray analysis to examine transcriptomic changes under drought, identifying thousands of genes that potentially mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.
2013-11-06 | E-GEOD-40998 | biostudies-arrayexpress
Project description:Characterization of porcine chromosomal regions harboring QTL for water holding capacity of meta by tiling arrays and mRNA-seq
| PRJNA246567 | ENA
Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture. Experiment Overall Design: Gene expression profiles were correlated with beef traits measured at the same cattle.
2008-11-01 | E-GEOD-9256 | biostudies-arrayexpress
Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture.
2008-10-06 | GSE9256 | GEO
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
2009-03-19 | GSE10753 | GEO
Project description:We used microarray analysis to examine transcriptomic changes upon dreb1a under drought, identifying hundreds of genes that potentially function downstream of DREB1A and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. DREB1a mutant (CS872453) were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest. Unopened flower samples were collected from drought treated plants, at day 3, 4, 5.
2013-11-06 | E-GEOD-43724 | biostudies-arrayexpress
Project description:Macaque species share over 93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g.,HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. To close this gap and enhance functional genomics approaches, we employed a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome-level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells (iPSCs) derived from the same animal. Reconstruction of the evolutionary tree using whole genome annotation and orthologous comparisons among three macaque species, human and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.
2020-05-04 | PXD018943 | Pride