Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA225934 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads were furhter trimmed for quality and lenght (>250 bp).
2012-11-11 | GSE25345 | GEO
Project description:Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads were furhter trimmed for quality and lenght (>250 bp). 15 samples examined in total from important plume zones of the aquifer sampled in Feb. 2006, Sep. 2008 and Jun. 2009 (5 every year of sampling).
2012-11-11 | E-GEOD-25345 | biostudies-arrayexpress
Project description:Four cDNA libraries from immature embryos, mature embryos, microspore derived embryos and mature leaves were constructed. cDNA were sequenced by the Roche-454 GS-FLX.
2017-01-11 | E-MTAB-3226 | biostudies-arrayexpress
Project description:We report how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted: 1) fractionated low LET γ radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET γ radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. For each experiment, the colon was resected and feces removed for microbial sequencing analysis on a Roche 454 Genome Sequencer FLX Titanium instrument (Microbiome Core Facility, Chapel Hill NC) using the GS FLX Titanium XLR70 sequencing reagents and protocols. Analysis of amplicon sequencing data was carried out using the QIIME pipeline. Low LET radiation, high iron diet, and spaceflight increased Bacteroidetes and decreased Firmicutes. Low LET radiation, high Fe diet, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Microbiota characteriztion in these models is a first step in understanding the impact of the space environment on intestinal health.
2015-11-30 | GSE68738 | GEO
Project description:Teladorsagia circumcincta transcriptome sequencing study, using Roche
454-Titanium
| PRJEB2633 | ENA
Project description:Propionibacterium freudenreichii is an important starter culture used in the manufacture of Swiss-type cheeses. We have generated the complete genome sequence of a Propionibacterium freudenreichii ssp. shermanii strain JS at the Institute of Biotechnology, University of Helsinki, by using a combination of pyrosequencing with GS FLX and GS FLX Titanium series reagents (Roche) and SOLiD 4 (Life Technologies), ABI 3130xl Genetic Analyzer (Life Technologies), and PacBio RS II (Pacific Biosciences) instruments. Initial genome annotation was carried out using RAST, and additional functional annotation information for each CDS was obtained from BLANNOTATOR, CDD, and KAAS. Accession number for genome sequence is PRJEB12148. This submission is for the transcriptome analysis of Propionibakcterium freudenreichii in cheese ripening under warm and cold conditions. The RNA reads were mapped to the reference genome PRJEB12148.
2016-04-14 | E-MTAB-4593 | biostudies-arrayexpress
Project description:Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). These results show high (R2 >0.9) intra-platform consistency across test sites, high inter-platform concordance (R2 >0.8) for transcriptome profiling, and a large set of novel splice junctions observed across all platforms. Also, we observe that protocols using ribosomal RNA depletion can both salvage degraded RNA samples and also be readily compared to polyA-enriched fractions. These data provide a broad foundation for standardization, evaluation and improvement of RNA-seq methods. Two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). Please note that the samples were named following the ABRF-Platform-Site-Sample-Replicate# format. For example, ABRF-454-CNL-A-1 means Sample A was run on 454 platform at Cornell and this is the first replicate, and ABRF-454-CNL-A-2 means the same exact sample was ran with same machine at same location and is 2nd replicate.
2014-05-14 | E-GEOD-48032 | biostudies-arrayexpress
Project description:Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). These results show high (R2 >0.9) intra-platform consistency across test sites, high inter-platform concordance (R2 >0.8) for transcriptome profiling, and a large set of novel splice junctions observed across all platforms. Also, we observe that protocols using ribosomal RNA depletion can both salvage degraded RNA samples and also be readily compared to polyA-enriched fractions. These data provide a broad foundation for standardization, evaluation and improvement of RNA-seq methods. Two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). Please note that the samples were named following the ABRF-Platform-Site-Sample-Replicate# format. For example, ABRF-454-CNL-A-1 means Sample A was run on 454 platform at Cornell and this is the first replicate, and ABRF-454-CNL-A-2 means the same exact sample was ran with same machine at same location and is 2nd replicate.
2014-05-14 | E-GEOD-48033 | biostudies-arrayexpress