|
| Biological samples |
|
| Frozen human kidney tissues |
The National Disease Research Interchange (NDRI) |
http://www.ndriresource.org/; RRID:SCR_000550 |
| Frozen human kidney tissues |
Gift of Life Michigan |
N/A |
|
| Chemicals, peptides, and recombinant proteins |
|
| 6x Homogenization Buffer |
In-house |
30mM CaCl2, 18 mM Mg(AC)2, 60mM Tris pH 7.8, 0.1mM PMSF, 1mM β-mercaptoethanol, 320mM Sucrose, 0.1mM EDTA, 0.1%NP40 |
| ATAC-Resuspension Buffer (RSB) |
In-house |
10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 1% BSA |
| PMSF |
Sigma |
P7626–1G |
| β-mercaptoethanol |
Sigma |
M6250–100ML |
| Iodixanol solution |
Sigma |
D1556–250ML |
| Calcium chloride |
Sigma |
21115–100ML |
| Magnesium acetate |
Sigma |
63052–100ML |
| EDTA |
Ambion |
AM9261 |
| Sucrose |
Sigma |
S7903–250G |
| Digitonin |
Sigma-Aldrich |
Product# 300410 |
| BSA |
Sigma-Aldrich |
Product# A2153 |
| NP-40 |
Thermofischer Scientific |
CAT# 85124 |
| Tris-HCL |
Thermofischer Scientific |
CAT# 15567027 |
| Sodium Chloride Solution |
Thermofischer Scientific |
CAT# AM9759 |
| Magnesium Chloride Solution |
Thermofischer Scientific |
CAT# AM9530G |
| Tween 20 |
Thermofischer Scientific |
CAT# 28320 |
| TD buffer |
Illumina |
20034198 |
| Transposase |
Illumina |
15027865 |
| RNAse inhibitor |
Thermofischer Scientific |
CAT# AM2696 |
| DAPI |
Thermofischer Scientific |
D1306 |
| Nuclei EZ lysis buffer |
Sigma Aldrich |
Product# NUC-101 |
|
| Critical commercial assays |
|
| MinElute Reaction Cleanup Kit |
Qiagen |
28206 |
|
| Deposited data |
|
| Raw and processed data for kidney tissues |
This paper |
GEO: GSE200047
|
| UK-Biobank GWAS summary statistics |
UK Biobank33
|
http://www.nealelab.is/uk-biobank/
|
| GWAS summary statistics for BP datasets |
NHGRI-EBI GWAS Catalog1
|
http://www.ebi.ac.uk/gwas/; RRID:SCR_012745 |
| Human Gene Annotation data from GENCODE |
GENCODE48
|
https://www.gencodegenes.org/; RRID:SCR_014966 |
| GTEx RNA-seq data for BP tissues |
GTEx Consortium32
|
http://commonfund.nih.gov/GTEx/; RRID:SCR_013042 |
| CIS-BP TFBS Motif data |
Weirauch et al.49
|
http://cisbp.ccbr.utoronto.ca; RRID:SCR_017236 |
| 1000 Genomes Project |
The 1000 Genomes Project Consortium50
|
http://www.1000genomes.org/; RRID:SCR_006828 |
| DNase-seq and ATAC-seq data for BP tissues |
ENCODE Project Consortium28
|
https://www.encodeproject.org/; RRID:SCR_015482 |
|
| Software and algorithms |
|
| BEDTools |
Quinlan & Hall51
|
https://github.com/arq5x/bedtools2; RRID:SCR_006646 |
| Bowtie2 |
Langmead & Salzberg52
|
RRID:SCR_016368 |
| cutadapt |
Martin53
|
RRID:SCR_011841 |
| FIMO |
Grant et al.54
|
https://meme-suite.org/meme/doc/fimo.html
|
| gkmQC |
Han et al.29
|
https://github.com/Dongwon-Lee/gkmQC
|
| LDSC |
Finucane et al.30
|
RRID:SCR_022801 |
| LS-GKM |
Lee26
|
https://github.com/Dongwon-Lee/lsgkm
|
| MACS2 |
Zhang et al.55
|
RRID:SCR_013291 |
| Picard Toolkit |
Broad Institute |
https://broadinstitute.github.io/picard/; RRID:SCR_006525 |
| Python 3.9.15 |
Python Software Foundation |
http://www.python.org/; RRID:SCR_008394 |
| R 3.6.2 |
The R Project for Statistical Computing |
https://www.r-project.org/; RRID:SCR_001905 |
| SAMTools |
Li et al.56
|
RRID:SCR_002105 |
|
| Other |
|
| Pipeline scripts |
This paper |
https://github.com/Dongwon-Lee/bph2; https://doi.org/10.5281/zenodo.8400966
|
| Supplemental Data |
This paper |
https://doi.org/10.5281/zenodo.8057373
|
