ATAC-seq
Reproducible inference of transcription factor footprints in ATAC seq and DNase seq datasets using protocol specific bias modeling
... lyzing ATAC-seq datasets employ a correction where the reads that align to the plus strand are shifted by + 4, and the reads that align to the minus strand are shifted by − 5 bases, to update the read start ...
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EpiMethylTag: simultaneous detection of ATAC seq or ChIP seq signals with DNA methylation
... conversion, ATAC-seq, and CTCF ChIPmentation with Nextera transposase [13, ...regular ATAC-seq and M-ATAC signal before bisulfite ...
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Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq
... Results: We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase‑accessible chromatin with high‑throughput sequencing (ATAC‑seq) as a ...
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Assessment of computational methods for the analysis of single cell ATAC seq data
... bulk ATAC-seq datasets with clear annotations from the bone marrow and erythropoiesis [7, 19, 20] using varying noise levels and read ...bulk ATAC- seq ...
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ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
... of ATAC-seq data can be sensitive to underlying biases within the data, as might be ...global ATAC distribution biases that were only thor- oughly eliminated through certain normalization meth- ods, ...
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A novel ATAC seq approach reveals lineage specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
... (a) ATAC-seq fragment size ...these ATAC-seq fragments is shown on the ...nucleosome-free ATAC-seq fragments at CTCF motif regions comparing control and BAF ...mononucleosome ...
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Identification of transcription factor binding sites using ATAC seq
... to ATAC-seq data of dendritic cell (DC) ...either ATAC-seq peaks or footprints by Wellington or ...by ATAC-seq peaks, Wellington or HINT-ATAC ...with ...
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Studying hematopoiesis using single-cell technologies
... Aorta-gonad-mesonephros; ATAC-seq: Assay for transposase-accessible chromatin with high-throughput sequencing; Baso: Basophil; CLP: Common lymphoid progenitors; CMP: Common myeloid progenitors; CNVs: Copy ...
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Recapitulation-like developmental transitions of chromatin accessibility in vertebrates
... using ATAC- seq ...in ATAC- seq read enrichments during embryogenesis ...the ATAC-seq reads were enriched at the transcription start sites (TSSs) of genes with low back- ground ...
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Chromatin accessibility and transcription dynamics during in vitro astrocyte differentiation of Huntington’s Disease Monkey pluripotent stem cells
... and ATAC-seq data, we hypothesize that, broadly speaking, there are two distinct stages of HD-mediated dysregulation that occur during astrocyte development: one in PSCs and the other beginning in the NPC ...
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Viraj_Rapolu_Thesis.pdf
... The WASP pipeline (van de Geijn et al) was used to perform allelic imbalance analysis for this project. Specifically, the mapping pipeline is used to mitigate mapping biases when aligning ATAC-seq reads to ...
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Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
... more ATAC-seq signals compared to the GF cells, suggest- ing a global increase of open chromatin in this ...GF-specific ATAC-seq signals showed a surprising enrichment for amino acid response ...
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NicE seq: high resolution open chromatin profiling
... and ATAC-seq (assay for transposase-accessible chromatin using sequencing) ...DNA. ATAC-seq uses a hyperactive Tn5 transposase which preferentially integrates its payload adaptor into ...
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Genomic effects of the vitamin D receptor: Potentially the link between vitamin D, immune cells, and multiple sclerosis
... 1; ATAC-seq, assay for transposase-acces- sible chromatin using sequencing; C/EBP, CCAAT/enhancer-binding protein; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; ChIP- seq, ...
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Chromatin accessibility: a window into the genome
... Functional annotation of accessible regions is factor- dependent and relies highly on the availability of accur- ate TF binding motifs and their relevant information content as well as the spatial and temporal ...
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PubMedCentral-PMC4931250.pdf
... including ATAC-seq on skeletal muscle, and transcriptome data across diverse tissues reveals that the tissue-specific genetic regulatory architecture of skeletal muscle is highly enriched in muscle ...
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Epigenetic mechanisms underlying maternal diabetes-associated risk of congenital heart disease
... protease inhibitor cocktail (11836170001, Sigma-Aldrich) and spun at 500 g for 5 minutes (4°C). Nuclear pellets were transposed with 25.0 μl Tagmentation DNA buffer, 2.5 μl Transposase enzyme (Nextera DNA library ...
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Detect accessible chromatin using ATAC-sequencing, from principle to applications
... Quality control of the ATAC-seq library should be per- formed prior to sequencing to guarantee that the library con- centration reaches the sequencing criteria. After library sequencing, raw reads are ...
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Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS seq) assay
... and ATAC-seq methods have several areas that can be improved upon to increase assay ...by ATAC-seq and its usage of the Tn5 transposome system, which was origin- ally developed for generating ...
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XL-DNase-seq: improved footprinting of dynamic transcription factors
... or ATAC-seq sample, had the potential to circumvent many of these issues with ChIP-based assays [4, 11, ...of ATAC-seq) profiles face differ- ent ...
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