Miseq Illumina paired-sequencing of 600-bp fragment from one ostrich (paired) female
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB24106 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Illumina Miseq paired-end sequencing (2x250) of 550 pb fragment from the genome of one ostrish
| PRJEB24169 | ENA
Project description:The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising, the removal of sequencing errors, is an important step in preprocessing amplicon sequencing data. The increasing popularity of the Illumina MiSeq platform for these applications requires the development of appropriate denoising methods.The newly proposed denoising algorithm IPED includes a machine learning method which predicts potentially erroneous positions in sequencing reads based on a combination of quality metrics. Subsequently, this information is used to group those error-containing reads with correct reads, resulting in error-free consensus reads. This is achieved by masking potentially erroneous positions during this clustering step. Compared to the second best algorithm available, IPED detects double the amount of errors. Reducing the error rate had a positive effect on the clustering of reads in operational taxonomic units, with an almost perfect correspondence between the number of clusters and the theoretical number of species present in the mock communities.Our algorithm IPED is a powerful denoising tool for correcting sequencing errors in Illumina MiSeq 16S rRNA gene amplicon sequencing data. Apart from significantly reducing the error rate of the sequencing reads, it has also a beneficial effect on their clustering into operational taxonomic units. IPED is freely available at http://science.sckcen.be/en/Institutes/EHS/MCB/MIC/Bioinformatics/ .
| S-EPMC4850673 | biostudies-literature
Project description:Background. Food can affect the microbial balance in the human intestine, and the ingestion of probiotics may play a role in the current obesity pandemic. The objective of our study was to determine if increased Lactobacillus spp. in the intestinal microflora of mice can promote growth and if changes in the intestinal microflora are associated with modifications in metabolism. Methodology. Female BALBc mice were divided between one control and two experimental groups and inoculated either once or twice with 4×1010 Lactobacillus per animal in PBS or with PBS alone. Fecal samples were collected and tested using qPCR to detect and quantify Lactobacillus spp., Bacteroidetes and Firmicutes. Gene expression by microarray and RT-PCR was studied in liver and adipose tissue. Finally, metabolic parameters in the plasma were tested. Principal Findings. In three independent experiments, we observed an increase in both weight gain and liver weight in mice inoculated with 4×1010 Lactobacillus. Inoculation with Lactobacillus sp. (ostrich) increased the Lactobacillus spp. and Firmicutes DNA copy number in feces. The transcriptional profile of liver tissue from mice inoculated with Lactobacillus sp. (ostrich) was enriched for Gene Ontology terms related to the immune response and metabolic modifications. The mRNA levels of fatty acyl synthase (Fas), sterol regulatory element binding factor 1 (Srebp1c), tumor necrosis factor alpha (Tnf), cytochrome P450 2E1 (Cyp2e1) and 3-phosphoinositide-dependent protein kinase-1 (Pdpk1) were significantly elevated in liver tissue in experimental group animals. In gonadal adipose tissue, the expression of leptin, peroxisome proliferator-activated receptor gamma (Pparg and Srebp1c was significantly higher in experimental group animals, whereas the expression of adiponectin was significantly lower. Conclusions. Alterations in the intestinal microbiota resulted in increased weight gain. Furthermore, increased Lactobacillus spp. in the intestinal microflora of mice inoculated with Lactobacillus sp. (ostrich) resulted in accelerated weight gain, liver enlargement and metabolic changes in the plasma, liver and adipose tissue.
2010-09-21 | GSE24219 | GEO
Project description:Genome sequencing for investigating genetic features of one female of african fisher eagle. The library and the sequencing were made at the Plateforme de Séquençage Haut Débit I2BC (Gif-sur-Yvette 91198 France.
| PRJEB27669 | ENA
Project description:Genome sequencing for investigating genetic features of one female of black-chinned hummingbird. The library and the sequencing were made at the Plateforme de Séquençage Haut Débit I2BC (Gif-sur-Yvette 91198 France.
| PRJEB27670 | ENA
Project description:Production of an ostrich-derived phage display library to capture the ostrich-derived single-chain variable fragment (scFv) antibodies
| PRJEB67560 | ENA
Project description:mice feces Illumina Miseq paired-end reads Raw sequence reads
| PRJNA1012556 | ENA
Project description:Background. Food can affect the microbial balance in the human intestine, and the ingestion of probiotics may play a role in the current obesity pandemic. The objective of our study was to determine if increased Lactobacillus spp. in the intestinal microflora of mice can promote growth and if changes in the intestinal microflora are associated with modifications in metabolism. Methodology. Female BALBc mice were divided between one control and two experimental groups and inoculated either once or twice with 4×1010 Lactobacillus per animal in PBS or with PBS alone. Fecal samples were collected and tested using qPCR to detect and quantify Lactobacillus spp., Bacteroidetes and Firmicutes. Gene expression by microarray and RT-PCR was studied in liver and adipose tissue. Finally, metabolic parameters in the plasma were tested. Principal Findings. In three independent experiments, we observed an increase in both weight gain and liver weight in mice inoculated with 4×1010 Lactobacillus. Inoculation with Lactobacillus sp. (ostrich) increased the Lactobacillus spp. and Firmicutes DNA copy number in feces. The transcriptional profile of liver tissue from mice inoculated with Lactobacillus sp. (ostrich) was enriched for Gene Ontology terms related to the immune response and metabolic modifications. The mRNA levels of fatty acyl synthase (Fas), sterol regulatory element binding factor 1 (Srebp1c), tumor necrosis factor alpha (Tnf), cytochrome P450 2E1 (Cyp2e1) and 3-phosphoinositide-dependent protein kinase-1 (Pdpk1) were significantly elevated in liver tissue in experimental group animals. In gonadal adipose tissue, the expression of leptin, peroxisome proliferator-activated receptor gamma (Pparg and Srebp1c was significantly higher in experimental group animals, whereas the expression of adiponectin was significantly lower. Conclusions. Alterations in the intestinal microbiota resulted in increased weight gain. Furthermore, increased Lactobacillus spp. in the intestinal microflora of mice inoculated with Lactobacillus sp. (ostrich) resulted in accelerated weight gain, liver enlargement and metabolic changes in the plasma, liver and adipose tissue. For microarray analysis, we used the livers from two LB1 and two control mice that had been euthanized 20 days after inoculation. We used a whole mouse genome oligomicroarray 4x44K kit (44,000 60-mer oligonucleotides) and performed a one-color microarray-based gene expression analysis, as previously described. Labeled RNAs (Low RNA Input Fluorescent Amplification Kit, Perkin Elmer) were deposited on slides and hybridized using an in situ Hybridization Plus Kit (Agilent Technologies) for 17 h. The arrays were scanned using a DNA Microarray Scanner G2505B (Agilent Technologies), and the image analysis and correction of intra-array signals were performed using Feature Extraction Software A.9.1.3 (Agilent Technologies). Microarray data analysis was performed using GeneSpring 10.01 with the default setting for inter-array normalization and inter-replicate corrections. To identify genes that were differentially expressed, we used a Student’s t-test with p<0.05, and an absolute fold change (FC) greater than 2.0 considered significant. An analysis of Gene Ontology (GO) terms was performed to identify any altered biological processes. Additional data analysis was performed using R software, version 2.8.1. RNA extraction and cDNA synthesis were performed as described above. Primers and probes to target the mouse genes for cytochrome P450 2E1 (Cyp2e1), 3-phosphoinositide-dependent protein kinase-1 (Pdpk1) and glyceraldehyde 3-phosphate dehydrogenase (Gapdh, used as a housekeeping gene) were purchased from Applied Biosystems. qPCR reactions were performed as described above. The relative amount of each examined mRNA was normalized to the Gapdh mRNA expression level and is expressed relative to the mean amount of the same mRNA in the control group.
2010-09-21 | E-GEOD-24219 | biostudies-arrayexpress
Project description:Genome sequencing of Plasmodium falciparum culture-adapted Cambodian field isolates PL1, PL2, PL5 and PL7.
| PRJEB8074 | ENA
Project description:The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in extant species and consistent with the Liushu Struthio sp. ootaxon. These findings push the preservation of ancient proteins back to the Miocene and highlight their potential for paleontology, paleoecology and evolutionary biology.
2022-12-29 | PXD035872 | Pride