Project description:We performed RNAseq and ATACseq on FACS isolated Col1a1-GFP lung mesenchyme in culture compared to directly sorted from lung tissue
Project description:μATACseq data generated from 100, 500 and 1,000 FACS-purified Atoh1-GFP expressing cerebellar granule precursors (CGPs) are consistent with those from 20,000 CGPs by the standard ATACseq protocol (R > 0.85), with comparable percentages of both the reads mapped to the promoters (±1000bp Transcription Start Sites), and to the distal elements. Of the peaks identified from the standard ATACseq method, more than 70% are detected among those from the μATACseq with as low as 100 cells. In addition, μATACseq lowers the sequencing cost by generating 10-fold fewer mitochondrial reads and up to 1.7-fold fewer PCR duplicates. Surprisingly, the μATACseq protocol is robust over a 10-fold difference in the transposase-to-cell ratios measured by (1) the fragment size distribution inferred from pair-end sequencing, (2) the depth of the predicted transcription factor footprints, (3) and the concordance between biological replicates. Further more, μATACseq is fast and convenient, does not require multiple washing steps or nuclear isolation, and demands only 20 minutes prior to DNA purification and sequencing library amplification.
Project description:B cells from tonsils of human donors were extracted for combined RNAseq+ATACseq from the same cell. One sample was prepared separately ("old") and is of lower quality, but still included. It primarily holds ATACseq information.
Project description:Tissue stem cells are required for homeostasis and wound repair throughout the entire lifespan. Multiple mechanisms have been extensively studied for the maintenance of stem cell quiescence. Here we use Omini-ATACseq and single cell ATACseq to study the stem cell quiescence at epigenetic level. We sought out to compare the open chromatin state in different cell lineages between control and Foxc1/Nfatc1 double knockout mice. The single cell ATACseq could further help infer the transcription regulation between enhancers and promoters interaction.
Project description:Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes. Histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), chromatin modifiers (p300), transcription factors (NR2F1, TFAP2A), chromatin accessibility (ATACseq) and gene expression (RNAseq) were assayed in CNCCs derived from iPSCs/ESCs from 2 chimpanzee and 3 human individuals.