Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology (Satpathy, Granja et al. 2019)

Link : https://www.nature.com/articles/s41587-019-0206-z

Please cite : Satpathy, Granja et al. , Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology (2019)

For current up to date scATAC-seq analysis https://github.com/GreenleafLab/ArchR

Downsampled test data for PBMCs is available (~500 MB)

Links To Supplementary Data

Notes

.rds file is an R binarized object to read into R use readRDS(filename)

scATAC-seq Hematopoiesis

scATAC-seq CD34 Hematopoiesis

scATAC-seq BCC Tumor Microenvironment

scATAC-seq BCC Tcells (Exhaustion)

If you want Tcell clusters get colData(se)$T_Cell_Cluster

Getting 10x scATAC-seq Bam Files

jianguozhou3 / 10x-scatac-2019 Goto Github PK

10x-scatac-2019's Introduction

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology (Satpathy*, Granja* et al. 2019)

Link : https://www.nature.com/articles/s41587-019-0206-z

Please cite : Satpathy*, Granja* et al. , Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology (2019)

For current up to date scATAC-seq analysis https://github.com/GreenleafLab/ArchR

Downsampled test data for PBMCs is available (~500 MB)

Links To Supplementary Data

Notes

scATAC-seq Hematopoiesis

scATAC-seq CD34 Hematopoiesis

scATAC-seq BCC Tumor Microenvironment

scATAC-seq BCC Tcells (Exhaustion)

Getting 10x scATAC-seq Bam Files

1. Go to NIH GEO Page : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129785&holding=F1000&otool=stanford.

2. Click on a sample (I am showing SU001_Tumor_Immune_Post).

3. Navigate down to the bottom and click on SRA link.

4. Navigate down and fine the run SRR.

5. Click on "Data Access" Tab and then navigate to "Original Format"

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology (Satpathy, Granja et al. 2019)

Please cite : Satpathy, Granja et al. , Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nature Biotechnology (2019)