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Project description:We developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by estrogen receptor α (ERα) in the human genome. We performed 454 and Illumina sequencing analyses. Keywords: Epigenetics Using 454, we examined 3 libraries: IHM001 (Estrogen Receptor ChIA-PET), IHM043 (Estrogen Receptor ChIP-PET) and IHM062 (IgG ChIA-PET) Using Illumina, we examined 4 libraries: IHM001 (Estrogen Receptor ChIA-PET replicate 1, Paired End Sequencing), IHH015 (Estrogen Receptor ChIA-PET replicate 2, Paired End Sequencing), H3K4me3 ChIP-Seq and RNA polymerase II ChIP-Seq
2009-09-11 | E-GEOD-18046 | biostudies-arrayexpress
Project description:We report transcriptional changes in grizzly bear muscle during hibernation (February) as compared to before (October). We used Gastrocnemius muscle biopsies taken during Febrary (hibernation) and the October before (activity) for mRNA extraction followed by 454, paired-end and single-end Illumina sequencing. Resulting reads were later mapped to human homologs and used for further analysis.
2019-12-31 | GSE63864 | GEO
Project description:We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation. Keywords: array CGH
2007-09-28 | GSE9002 | GEO
Project description:We developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by estrogen receptor α (ERα) in the human genome. We performed 454 and Illumina sequencing analyses. Keywords: Epigenetics
2009-09-11 | GSE18046 | GEO
Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.
2018-02-01 | E-MTAB-6054 | biostudies-arrayexpress
Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.
2018-02-02 | E-MTAB-6404 | biostudies-arrayexpress
Project description:This study reports on the generation of a transgenic mouse which is characterized by early-onset angle-closure glaucoma. The phenotype is due to the transgene insertion site which is proximal to the genes encoding AP-2 and AP-2, two proteins present in the retina and corneal epithelium. This leads to a reduction in AP-2 levels, which is likely to are responsible for the glaucomatous phenotype. Here we provide paired-end raw DNA-Seq reads of the transgenic mouse genome.
2017-03-10 | E-MTAB-5502 | biostudies-arrayexpress
Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.
2015-04-10 | E-GEOD-52170 | biostudies-arrayexpress
Project description:We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation. Keywords: array CGH 2 samples were analyzed with 8 different Nimblegen chips (385k); thus ~30M probes were used to interrogate copy number variants in NA15510 (using NA18505 as control) at high resolution.
2007-09-28 | E-GEOD-9002 | biostudies-arrayexpress
Project description:Deep sequencing of total RNA extracted from the genital discs of males for each of the following strains : Drosophila sechellia, Drosophila mauritiana, hybrid introgression line 3Q1(A) and hybrid introgression line Q1(A) Analysis of poly(A)+ RNA for three independent biological replicates of sequencing libraries for each of the following strains: D. sechellia w, D. mauritiana P-insertion Q1, hybrid introgression line 3Q1(A), and hybrid introgression line Q1(A). Male genital discs were obtained as described above, and total RNA was extracted using RNAqueousM-CM-^BM-BM-.-Micro Kit (Ambion). Poly(A)+ transcripts were isolated subsequently using MicroPoly(A)PuristM-CM-"M-BM-^DM-BM-" Kit (Ambion). To facilitate normalization of reads across our samples, at this stage of library construction we spiked-in small amounts of exogenous RNA from ArrayControlM-CM-"M-BM-^DM-BM-" Kit (Ambion) into each sample of poly(A)+ RNA. Paired-end sequencing was carried out by loading the samples onto four lanes (three samples per lane) of a flow cell and run on an Illumina Genome Analyzer IIx sequencer using 72 cycles per end of each paired-end read. Biological replicates of each genotype were loaded onto separate lanes.
2011-07-22 | E-GEOD-28663 | biostudies-arrayexpress