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)

https://jeffgranja.s3.amazonaws.com/10x-scATAC-share/10x-scATAC-Downsampled-PBMC-hg19-data.zip

Links To Supplementary Data

Notes

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

SummarizedExperiment is a class in R see :
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html

deviations (TF chromVAR) is a class in R see :
https://bioconductor.org/packages/release/bioc/html/chromVAR.html

scATAC-seq Hematopoiesis

scATAC Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/scATAC_Heme_All_SummarizedExperiment.final.rds

chromVAR Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/chromVAR_Heme_All_SummarizedExperiment.final.rds

Cicero Log2 Gene Acitvity Scores Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/Log2_Gene_Activity_Heme_All_SummarizedExperiment.final.rds

scATAC-seq CD34 Hematopoiesis

scATAC Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/scATAC_CD34_BM_SummarizedExperiment.final.rds

scATAC-seq BCC Tumor Microenvironment

scATAC Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/scATAC_TME_All_SummarizedExperiment.final.rds

chromVAR Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/chromVAR_TME_All_SummarizedExperiment.final.rds

Cicero Log2 Gene Acitvity Scores Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/Log2_Gene_Activity_TME_All_SummarizedExperiment.final.rds

scATAC-seq BCC Tcells (Exhaustion)

scATAC Summarized Experiment :
https://changseq.s3.amazonaws.com/Jeff/10x_ScATAC/scATAC_TME_TCells_SummarizedExperiment.final.rds

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

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"