Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

µATACseq: ATACseq with as few as 100 cells

ABSTRACT: µATACseq: ATACseq with as few as 100 cells

PROVIDER: PRJNA631703 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

µATACseq: ATACseq with as few as 100 cells

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.

2021-07-09 | GSE150275 | GEO

ATACseq of kdrl-GFP+ endothelial cells in 28hpf zebrafish embryos

Project description:The goal of this study is to analyse the open chromatin regions via ATACseq in zebrafish embryonic endothelial cells at 26-27hpf using Tg(Kdrl:GFP) transgenic zebrafish embryos. 40000-50000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. DNA was purified using the QIAquick PCR purification kit (Qiagen). Fragments were amplified for 16 cycles.

2020-01-16 | GSE143763 | GEO

ATACseq of IMR32 cells treated with ISX or solvent control

Project description:IMR32 cells were treated with DMSO/ISX and open chromatin regions were assessed via ATACseq

2023-01-17 | E-MTAB-11633 | biostudies-arrayexpress

Single cell ATACseq of lung dendritic cells from hyperglycemic mice

Project description:We performed single cell ATACseq to measure chromatin accessibility in different subsets of lung dendritic cells hyperglycaemic mice. We used genetic model to achieve hyperglycaemia and compared wild type and Akita mice.

2023-06-29 | E-MTAB-11392 | biostudies-arrayexpress

A microfluidic device for epigenomic profiling using 100 cells

Project description:We developed the microfluidic-oscillatory-washing-based ChIP-Seq (MOWChIP-Seq) protocol. We achieved genome-wide mapping of histone modifications (H3K4me3 and H3K27ac) with as few as 100 cells. Moreover, the automated microfluidic platform dramatically reduced assay time and has a potential for future scale-up.

2015-07-21 | GSE65516 | GEO

ATACseq of human basophils, B cells and CD34-derived basophils

Project description:human basophils and B cells (that were purified to >98% homogeneity) and CD34-derived basophils were processed for ATACseq

2019-11-08 | GSE138607 | GEO

ATACseq

Project description:ATACseq data for this study.

| EGAS00001007166 | EGA

ATACseq analysis of M07e cells and patient derived AMKL cells

Project description:ATACseq analysis of M07e cells and patient derived AMKL cells

| PRJNA543761 | ENA

ATACseq and RNAseq of mouse CD4 T cells

Project description:ATACseq and RNAseq of mouse CD4 T cells