Captive panda feces from two different bases
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA430178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6479570.fastq.gz | Fastqsanger.gz | |||
| SRR6479580.fastq.gz | Fastqsanger.gz | |||
| SRR6479590.fastq.gz | Fastqsanger.gz | |||
| SRR6479571.fastq.gz | Fastqsanger.gz | |||
| SRR6479581.fastq.gz | Fastqsanger.gz |
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Project description:Gene differential expression studies can serve to explore and understand the laws and 16 characteristics of animal life activities, and the difference in gene expression between different 17 animal tissues have been well demonstrated and studied. However, for the world-famous rare 18 and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood 19 and spleen has been reported separately. Here, in order to explore the transcriptome differences 20 between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, 21 lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 22 platform. The comparative analysis of the inter-tissue gene expression patterns was carried out 23 based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, 24 Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction 25 (PPI) network were performed according to the identified differentially expressed genes (DEGs). 26 We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 27 18,701 genes, including 3492 novel genes. With corrected p-value < 0.05 and |log2FoldChange| > 28 2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, 29 lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and 30 ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the 31 spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI 32 network. The results of the analyses showed a similar gene expression pattern between the spleen 33 and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome 34 resources of the giant panda, and it provided a valuable resource for further genetic research or 35 other potential research.
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Project description:Next generation sequencing reveal profiles in H3K27me3 and expression levels between WT and panda mutant, anti-Flag ChIP reveal the binding sites of PANDA protein
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Project description:Background: Aquaculture of the black tiger prawn Penaeus monodon remains severely constrained by an almost total dependence on wild-caught broodstock. Reliance on wild-caught broodstock stems, for the most part, from reduced reproductive potential of captive-reared females. Reproductive performance of captive-reared females is usually characterised by longer latency period, lower egg production, egg hatch rates and post-larval survivorship compared with their wild-caught counterparts. Improved understanding of the cellular and associated molecular events occurring during peneaid ovarian maturation could therefore be fundamental to improving reproductive success of captive-reared animals. Methodology/Principle Findings: In support of other studies, our histological analyses of developing oocytes revealed differences between wild-caught and captive-reared P. monodon, including reduced lipid accumulation in oocytes of captive-reared animals. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Custom oligonucleotide microarrays were constructed and screened with transcripts derived from the ovary, cephalothorax and eyestalk from animals of all ovarian maturation stages. Ovarian maturation-related differential expression patterns were observed for 111 transcripts, with 53 transcripts displaying differential expression between wild-caught and captive-reared animals. Notably transcripts encoding vitellogenin - the major egg yolk protein precursor, and a lipid storage droplet protein (which we named pmLSD) which is involved in lipid accumulation, were found to be more highly expressed in wild-caught animals. pmLSD transcripts localise to pre-vitellogenic oocytes of wild-caught animals and the pmLSD protein is exclusively localised to the surface of lipid droplets of oocytes at vitellogenic and cortical rod stages. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Target preparation and microarray hybridisation. Ovarian RNA samples from nine wild-caught animals representing six ovarian maturation stages (P, 2, 24, V, R, E) were used in microarray hybridisations. Similarly, RNA samples from three captive-reared animals representing four maturation stages (P, 24, V, E) were used in microarray hybridisations. For wild-caught animals, samples from each ovarian maturation stage were pooled into groups of four and five, enabling two hybridisations. For captive-reared animals, samples from each ovarian maturation stage from all three animals were pooled enabling one hybridisation for each stage. Importantly, as the four stages for captive-reared animals were (1) pre-ablation pre-vitellogenic, (2) post-ablation pre-vitellogenic, (3) post-ablation vitellogenic, (4) post-ablation vitellogenic with cortical rods, this arrangement allowed for 2 samples of captive-reared pre-vitellogenic and 2 samples of captive-reared vitellogenic, thereby enabling t-tests between samples, while also allowing analysis across the whole 4 stages via cluster analysis. All hybridisations were single channel hybridisations conducted using equal amounts of RNA pooled from each individual.
2011-09-01 | E-GEOD-31862 | biostudies-arrayexpress
Project description:Background: Aquaculture of the black tiger prawn Penaeus monodon remains severely constrained by an almost total dependence on wild-caught broodstock. Reliance on wild-caught broodstock stems, for the most part, from reduced reproductive potential of captive-reared females. Reproductive performance of captive-reared females is usually characterised by longer latency period, lower egg production, egg hatch rates and post-larval survivorship compared with their wild-caught counterparts. Improved understanding of the cellular and associated molecular events occurring during peneaid ovarian maturation could therefore be fundamental to improving reproductive success of captive-reared animals. Methodology/Principle Findings: In support of other studies, our histological analyses of developing oocytes revealed differences between wild-caught and captive-reared P. monodon, including reduced lipid accumulation in oocytes of captive-reared animals. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Custom oligonucleotide microarrays were constructed and screened with transcripts derived from the ovary, cephalothorax and eyestalk from animals of all ovarian maturation stages. Ovarian maturation-related differential expression patterns were observed for 111 transcripts, with 53 transcripts displaying differential expression between wild-caught and captive-reared animals. Notably transcripts encoding vitellogenin - the major egg yolk protein precursor, and a lipid storage droplet protein (which we named pmLSD) which is involved in lipid accumulation, were found to be more highly expressed in wild-caught animals. pmLSD transcripts localise to pre-vitellogenic oocytes of wild-caught animals and the pmLSD protein is exclusively localised to the surface of lipid droplets of oocytes at vitellogenic and cortical rod stages.
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