Project description:Mammalian genome encodes approximately 1,700 transcription factors (TFs), 1,300 out of which have sequence specific binding motifs. Transcription in mammalian cells is regulated by the recruitment of TFs to specific cis-regulatory elements. In spite of consistent efforts on the function of individual TF, the question still remains how TFs bind to DNA and form enhancer. Here, we try to solve this problem by investigating the relationship between TF binding pattern and chromatin accessibility (ATAC-Seq). We first systematically acquired ATAC-Seq dataset as well as matched RNA-Seq dataset from different mouse primary tissues. A comprehensive TF binding map was built for each tissue/cell type by genomic approaches.

2022-07-21 | GSE199410 | GEO

Effect of mithramycin on chromatin accessibility (ATAC-Seq)

Project description:Effect of mithramycin on chromatin accessibility (ATAC-Seq)

| PRJNA693316 | ENA

Effect of mithramycin on chromatin accessibility (ChIP-Seq)

Project description:Effect of mithramycin on chromatin accessibility (ChIP-Seq)

| PRJNA765332 | ENA

SNP effect on chromatin accessibility (ChIP-Seq)

2022-07-21 | GSE199516 | GEO

SNP effect on chromatin accessibility (ATAC-Seq)

2022-07-21 | GSE199430 | GEO

Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [RNA-seq]

Project description:Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas. 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.

2015-05-07 | E-GEOD-68102 | biostudies-arrayexpress

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