KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Adult Human Tissue Samples | ENTEx Collaboration | https://www.encodeproject.org/entex-matrix/?type=Experiment&status=released&internal_tags=ENTEx |
| Chemicals, peptides, and recombinant proteins | ||
| Tn5 transposase | QB3 Macrolab at UC Berkeley | N/A |
| SPRISelect reagent | Beckman Coulter | Cat# B23319 |
| DRAQ7 | Cell Signaling | Cat# 7406 |
| NEBNext High-Fidelity PCR Master Mix | topNEB | Cat# M0541L |
| LightCycler 480 SYBR Green I Master Mix | Roche | Cat# 04707516001 |
| Critical commercial assays | ||
| gentleMACS Octo Dissociator | Miltenyi | Cat# 130-095-937 |
| Deposited data | ||
| sci-ATAC-seq data of human adult tissues | This paper | GEO: GSE184462 |
| sci-ATAC-seq data of human lung samples | (Wang et al., 2020) | dbGaP: phs001961 |
| sci-ATAC-seq data of human heart samples | (Hocker et al., 2021) | dbGaP: phs002204 |
| sci-ATAC-seq data of human islet samples | (Chiou et al., 2021) | GEO: GSE160472 |
| sci-ATAC-seq data of human fetal tissues | (Domcke et al., 2020) |
https://descartes.brotmanbaty.org/bbi/human-chromatin-during-development/ dbGaP: phs002003 |
| raw data used to produce the figures | This paper | Mendeley Data: 10.17632/yv4fzv6cnm.1 |
| Oligonucleotides | ||
| Custom Tagmentation Oligos | This paper | Table S18 |
| Custom PCR Primers | This paper | Table S18 |
| Custom Sequencing Primers | This paper | Table S18 |
| Software and algorithms | ||
| BWA version 0.7.17 | (Li and Durbin, 2009) | https://github.com/lh3/bwa |
| Samtools version 1.9 | (Danecek et al., 2021) | https://github.com/samtools/samtools |
| Taiji version 1.3.0 | (Zhang et al., 2019) | https://github.com/Taiji-pipeline/Taiji |
| Python package: taiji-utils version 0.2.3 | This paper | https://pypi.org/project/taiji-utils/ |
| liftOver | (Kent et al., 2002) | http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver |
| ATACdemultiplex version 0.46.12 | This paper | https://gitlab.com/Grouumf/ATACdemultiplex/ |
| bedGraphToBigWig | (Kent et al., 2002) | http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig |
| R version 4.0.5 | R Foundation for Statistical Computing | https://www.r-project.org/ |
| Python version 3.8 | Python Software Foundation | https://www.python.org/ |
| Python package: umap-learn version 0.5.0 | https://pypi.org/project/umap-learn/ | |
| Python package: scrublet | (Wolock et al., 2019) | https://github.com/swolock/scrublet |
| GREAT version 4.0.4 | (McLean et al., 2010) | http://great.stanford.edu/public/html/ |