| Antibodies |
| Bacterial and Virus Strains |
| Biological Samples |
|
|
| Chemicals, Peptides, and Recombinant Proteins |
| Plasmocin |
Invivogen |
ant-mpt-1 |
| Tn5 transposase |
Synthesized using protocol in Picelli et al., 2014
|
N/A |
| SPRI beads |
GE Healthcare Life Sciences; prepared as in (Rohland and Reich, 2012) |
#65152105050250 |
| Critical Commercial Assays |
| Zymo DNA Clean & Concentrator-5 kit |
Zymo Research |
D4013 |
| Deposited Data |
| Raw and analyzed data |
This paper |
GEO: GSE130450
|
| Human reference genome hg19 |
Lander et al., 2001 |
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| Mouse reference genome mm9 |
Mouse Genome Sequencing Consortium et al., 2002 |
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/ |
| ENCODE human genome (hg19) blacklists |
ENCODE Project Consortium, 2012 |
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz, http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz
|
| ENCODE mouse genome (mm9) blacklist |
ENCODE Project Consortium, 2012 |
http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz |
| List of human housekeeping genes |
Eisenberg and Levanon, 2013 |
http://www.tau.ac.il/~elieis/HKG/HK_genes.txt |
| GM12878 chromatin states |
Parker et al., 2013 |
https://research.nhgri.nih.gov/manuscripts/Collins/islet_chromatin/hg19/ChromHMM/GM12878_chromHMM.bb |
| ENCODE IDR ChIP-seq peaks |
ENCODE Project Consortium, 2012; Li et al., 2011; Sloan et al., 2016
|
https://www.encodeproject.org |
| Public human and mouse ATAC-seq data |
See Table S2
|
See Table S2
|
| Experimental Models: Cell Lines |
| Human GM12878 cells |
Coriell |
GM12878 https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878
|
| Experimental Models: Organisms/Strains |
| Oligonucleotides |
| Recombinant DNA |
| Software and Algorithms |
| Ataqv (v. 1.1.0) |
This paper |
https://github.com/ParkerLab/ataqv |
| fastx-toolkit (v. 0.0.14) |
Not published |
http://hannonlab.cshl.edu/fastx_toolkit/ |
| cta (v. 0.1.2) |
Not published |
https://github.com/ParkerLab/cta |
| Bwa (v. 0.7.15) |
Li and Durbin, 2009 |
https://sourceforge.net/projects/bio-bwa/ |
| samtools (v. 1.7) |
Li et al., 2009 |
https://github.com/samtools/samtools |
| Picard MarkDuplicates (v. 2.18.27) |
Not published |
http://broadinstitute.github.io/picard |
| MACS2 (v. 2.1.1.20160309) |
Zhang et al., 2008 |
https://github.com/taoliu/MACS |
| Bedtools (v. 2.27.1) |
Quinlan, 2014 |
https://github.com/arq5x/bedtools2 |
| bigBedToBed (v. 1) |
Kent et al., 2010 |
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369 |
| bedGraphToBigWig (v. 4) |
Kent et al., 2010 |
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369 |
| MASS R package (v. 7.3-50) |
Venables and Ripley, 2002 |
https://cran.r-project.org/ |
| Other |
| Resource website for the ataqv manuscript |
This paper |
https://github.com/ParkerLab/ataqv-2019 |
