Cell Ranger ATAC versions 2.1 supports libraries generated by the Chromium Single Cell ATAC v1, v1.1 Next GEM, and v2 reagent kits. Workflows 10x Genomics recommends using the pipeline analysis programs in order, starting withcellranger-atac mkfastqfor demultiplexing the raw base call (BCL) files...
Pott, S., and Lieb, J.D. (2015). Single-cell ATAC-seq: strength in numbers. GenomePott, S.; Lieb, J.D. Single-cell ATAC-seq: Strength in numbers. Genome Biol. 2015, 16, 172, doi:10.1186/s13059-015-0737-7.Pott S, Lieb JD. Single-cell ATAC-seq: strength in numbers. Genome...
scores, while HyDrop and s3-ATAC scored markedly lower (Fig.2kand Extended Data Fig.1g). The most common PBMC types, including B cells, T cells and CD14+monocytes, were recovered by all techniques. However, the differences between methods became evident when focusing on rare cell types, suc...
此外,ezSingleCell允许不同模块在统一界面内进行交互,接受多种格式的数据输入,例如文本格式(csv 和 tsv)或 10x Cell Ranger/Space Ranger/Cell Ranger-ATAC 输出,并返回可供发布的图表。 ezSingleCell web服务器概述 ezSingleCell对现有的SciAp、ICARUS、CELLAR等单细胞数据分析web服务器进行了以下改进:1)包含更大...
ezSingleCell在以下方面改进了现有的单细胞数据分析平台:首先,ezSingleCell涵盖了更广泛的单细胞数据分析,包括单细胞多组学、单细胞ATAC-seq和空间转录组学。其次,ezSingleCell提供了超出基本分析流程的高级分析功能,如差异基因表达分析、基因集富集、细胞类型相似性和细胞间通讯。
当然,通量还是比较小。但不可否认的是,现在很多非RNA类Single Cell测序,仍然在采用这样的技术,如Single Cell DNA-Seq,Single Cell ATAC-Seq等,都是采用此技术进行单细胞分选后再分别用不同试剂盒建库。所以可以说,至少在10X和BD,或者其他企业推出有效的Single DNA测序技术之前,C1仍然会是市场上的重要组成部分。
Single-Cell ATAC-Seq Identify chromatin accessibility in the epigenome by profiling thousands of single cells in parallel, and discover how chromatin structure and DNA-binding proteins regulate gene expression in varying states and cellular processes. Learn More Single-Cell Immuno-Profiling Examine the...
Cell Ranger ATAC pipeline has two cut sites: the start position of the fragment, and the end position of the fragment. These are the locations where the ATAC enzyme attached to open chromatin. For each cut site, the Peak Viewer imputes an open region, where the chromatin is presumed to ...
Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of ear
2017年7月,奥地利研究人员在Nature Methods上发表“Pooled CRISPR screening with single-cell transcriptome readout (doi:10.1038/ nmeth.4227)”文章,创造性地将CRISPR-Cas9和单细胞RNA测序两种极有前景的基因组学领域结合在一起,发明了这种被称作CROP-seq的单细胞测序方法 (CRISPR droplet sequencing, CRISPR液滴测...