Validation of THS-seq method, and comparison of published ENCODE DNase-seq data, self-generated ATAC-seq data and published ATAC-seq data, and THS-seq data for quantitation of chromatin accessibility.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE72089 | GEO | 2016/01/09
SECONDARY ACCESSION(S): PRJNA293169
REPOSITORIES: GEO
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Project description:To investigate the specificity of the Tn5 transposome with short adaptor DNAs under the non-crosslinked condition, we conducted ATAC-seq using alternative 19 bp adaptor DNAs (IE and OE) harboring 7 nucleotide differences between them (Maggie.JMB.1998), which allowed for specific PCR amplification without losing the superior enzymatic activity.
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Project description:Two methods Fluorescence Activated Cell Sorting (FACS) and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) are combined to analyse the chromatin accessibility of Lateral Organ Founder Cells (LOFCs) in the peripheral zone of the apetala1 cauliflower double mutant Arabidopsis inflorescence meristem. Genome-wide we observed a striking correlation between Transposase Hypersensitive Sites (THS) detected in ATAC-seq and DNase I Hypersensitive Sites (DHS), covering mostly extended regions substructured into several individual THS that correspond to phylogenetically conserved sequence, enhancer elements and binding sites of MADS-box transcription factors. Relative to available RNA-seq data, chromatin configuration changes according to gene activation or repression, i.e. at cellular resolution chromatin regions gain or lose Tn5 transposase accessibility in direct correlation with gene expression levels. A pronounced THS priority immediately upstream of the transcription start and reduced numbers of THSs in the transcription unit are complementary to established H3K4me3 activation or H3K27me3 repressive marks. At this resolution, the FACS/ATAC-seq combination should be widely applicable to detect chromatin changes in course of cell type specification and facilitate the detection of regulatory promoter elements in plant promoters.
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Project description:A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. We further reveal the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia, chromatin accessibility reveals distinctive regulatory evolution in pre-leukemic HSCs (pHSCs), leukemia stem cells, and leukemic blasts. These leukemic cells demonstrate unique lineage infidelity, confirmed by single cell regulomes. We further show that pHSCs have a competitive advantage that is conferred by reduced chromatin accessibility at HOXA9 targets and is associated with adverse patient outcomes. Thus, regulome dynamics can provide diverse insights into human hematopoietic development and disease. ATAC-seq profiles of hematopoietic and leukemic cell types, across 13 normal hematopoietic cell types and 3 acute myeloid leukemia cell types. The complete data set contains a total of 132 samples.
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Project description:Assay for Transposable Accessible Chromatin (ATAC) reveals a genome wide view of areas of open chromatin at very high resolution, which are often associated with regulatory activity. The ATAC-seq technology uses a Tn5 transposase loaded with nex-generation sequencing primers in order to simultaneously fragment areas of open chromatin and ligate adapters.
2015-01-06 | E-GEOD-61065 | biostudies-arrayexpress
Project description:To establish an ultra-high-throughput single cell chromatin accessibility profiling method that is cost-effective and widely accessible, we built on sci-ATAC-seq (Cusanovich, D. A. et al. Science. 2015; Amini, S. et al. Nature Genetics. 2014) and SPLIT-seq (Rosenberg, A. B. et al. Science. 2018) to design SPATAC-seq, which in situ label chromatin fragment in the same single cell through combinatorial barcoding. Briefly, in SPATAC-seq, (1) fixed nuclei are transposed in 48 different wells by 48 unique Tn5 transposase, which containing barcoded adaptors and 5'-phosphorylation; (2) the nuclei from all wells are collected and redistributed into second and third 48-well plate in turn, where the next two rounds of indexing are achieved through into either end of the custom transposome, which result in the generation of more than 110,000 (48^3) unique barcode combinations. (3) the nuclei are pooled, split into sublibraries and lysed, and the DNA was amplified by polymerase chain reaction (PCR), which introduce illumina sequencing barcodes and complete libraries construction. (4) After sequencing, fastq files were demultiplexed according to the same four-barcode combinations. For profiling more cells in one sublibrary, we can increase the number of barcode combinations by increase the number of indexing of each round to 96, which can produce about 1 million combinations. To assess the fidelity of SPATAC-seq, we performed a species-mixing experiment with cultured human (K562) and mouse (Hepa) cells. Here, we tagged mixed permeabilized nuclei with only 8 barcoded transposome. In round 4, we generated eight sublibraries with different cell-recovery targets, which can be used to evaluating the stability of this method and the correlation between real doublet rates and theoretical value.
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