Genome sequencing cryptic Eimeria OTUs from chickens
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ABSTRACT:
PROVIDER: PRJEB40060 | ENA |
REPOSITORIES: ENA
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Project description:To determine microbiota composition associated with loss of KDM5 in intestine, we carried out 16S rRNA seq analyses of dissected intestine from wildtype and kdm5 mutant. [GSM2628181-GSM2628190]. A total of 78 operational taxonomic units (OTUs) were identified in the sequence data. There were about 15 genera much less abundant in kdm5 mutant compared to wildtype. The kdm5 mutant were sensitive to pathogen. To confirm the microbiota associated with loss of KDM5 in intestine, 16S rRNA of new flies were sequenced and analyzed by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China) [GSM3243472-GSM3243481]. A total of 107 operational taxonomic units (OTUs) were identified in the sequence data. There were about 20 genera much less abundant in kdm5 mutant compared to wildtype. To confirm the microbiota associated with loss of KDM5 drosophila feeding with Lactobacillus plantarum, 16S rRNA of kdm5 mutant flies were sequenced and analyzed by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China) [GSM3263522-GSM3263527]. A total of 92 operational taxonomic units (OTUs) were identified in the sequence data. To confirm the microbiota associated with KDM5 knockdown in intestine, 16S rRNA of Myo1A-Gal4TS/+ and Myo1A-Gal4TS/+;+/kdm5RNAi flies were sequenced and analyzed by Biomarker Co. Ltd. (Beijing, China). [GSM3507915-GSM3507924]. A total of 50 operational taxonomic units (OTUs) were identified in the sequence data. There was a significant different based on the genus level between two groups.
2019-02-08 | GSE98944 | GEO
Project description:Avian coccidiosis is a major disease of poultry caused by the intestinal protozoa Eimeria. Aviagen line A and line B birds show differential susceptibility to Eimeria infection, with line B birds exhibiting higher lesion scores and mortality. The objective of this study was to examine differential intestinal gene expression between line A and B chicks in response to a challenge with Eimeria maxima. Following challenge with 1 x 10^4 oocysts/chick, greater than 40% of line A chicks had lesion scores of 0 to 1 (on 0 to 4 scale), similar to controls. In contrast, all line B challenged chicks at this same dose had lesion scores of 2 to 4.
2011-07-01 | GSE25588 | GEO
Project description:Partial 18S rDNA and COI sequences from cryptic Eimeria species.
| PRJEB23613 | ENA
Project description:Avian coccidiosis is a major disease of poultry caused by the intestinal protozoa Eimeria. Aviagen line A and line B birds show differential susceptibility to Eimeria infection, with line B birds exhibiting higher lesion scores and mortality. The objective of this study was to examine differential intestinal gene expression between line A and B chicks in response to a challenge with Eimeria maxima. Following challenge with 1 x 10^4 oocysts/chick, greater than 40% of line A chicks had lesion scores of 0 to 1 (on 0 to 4 scale), similar to controls. In contrast, all line B challenged chicks at this same dose had lesion scores of 2 to 4. Total RNA was extracted from the jejunum of control and challenged chicks from both lines A and B. Microarrays were used for detecting the expression-changed genes which responsed to the Eimeria challenge. Samples included: four control A chicks, two challenged A chicks with a lesion score of 1 (A/LS1), two challenged A chicks with lesion scores of 3 to 4 (A/LS3-4), four control B chicks, two challenged B chicks with lesion scores of 2 (B/LS2-3) and two challenged B chicks with lesion scores of 4 (B/LS4). The DNA microarrays were processed at the Virginia Bioinformatics Institute (Virginia Tech) core facility. The raw array data were normalized using GC-robust multiple array (GC-RMA) normalization. Analysis of variance was used for differentially expressed genes based on Welch ANOVA (P < 0.05) and probe set lists were ordered using the fold change analysis provided by GeneSpring software.
2011-07-01 | E-GEOD-25588 | biostudies-arrayexpress
Project description:Eimeria are obligate intracellular protozoan parasites which can affect chickens. After exposure to Eimeria chickens establish (partial) protective immunity to the homologues strain. In this paper we investigate the process responsible for Eimeria protection. In order to find host reactions specificly involved in protection to homologous re-infection we investigated the host reactions after primary infection and a homologous or heterologous secondary infection.<br><br>Broilers were mock infected or infected with E.maxima (Max) at one week of age. Two weeks later broilers were mock infected, infected with E.maxima or E.acervulina. Oocyst output, T-cell population and cytokine mRNA expression profiles and Eimeria DNA profiles were measured 2, 4 and 7 days pi. Specific regulation of gene expression profiles was monitored by a whole genome oligo-array containing 20.673 oligoï¾´s at 8 and 24 hours pi.<br><br>
2009-08-01 | E-MEXP-1972 | biostudies-arrayexpress
Project description:Here we report 16s rRNA data in gut microbiota of hepatocellular carcinoma (HCC) patients with HBV induced HCC (HBVC) and non-HBV induced HCC (NHBVC) compared with healthy volunteers. A total of 2047 operational taxonomic units (OTUs) were identified in the sequence data. Our data shows that the NHBVC patients harbor lower anti-inflammatory bacteria and more pro-inflammatory bacteria, while the HBVC patients harbor more anti-inflammatory bacteria.
2019-02-27 | GSE108847 | GEO
Project description:Here we report 16S rRNA data in gut microbiota of autism spectrum disorders compared with healthy volunteers. A total of 1322 operational taxonomic units (OTUs) were identified in the sequence data. The Bacteroidetes and Firmicutes were both dominated phylum in ausitic subjects and healthy controls. Phylum level analysis showed a clear alteration of the bacterial gut community in ASD characterized by a higher Firmicutes (P < 0.05), Proteobacteria (P < 0.001), and Actinobacteria (P < 0.001) than that in healthy controls. However, Bacteroidetes were significantly decreased in ASD patients (P < 0.001).
2020-09-30 | GSE113690 | GEO