|
Antibodies
|
| anti-p65 |
Cell Signaling |
Cat#8242 |
| anti-PDX1 |
Cell Signaling |
Cat#5679 |
| anti-BMAL1 |
J. Bass, Millipore |
Cat#ABE2599 |
| anti-SIN3A |
Cell Signaling |
Cat#8056S |
| anti-Histone H3 |
Cell Signaling |
Cat#9715 |
| anti-GAPDH |
Cell Signaling |
Cat#5174 |
| HRP-linked anti-rabbit IgG |
Cell Signaling |
Cat#7074 |
|
RNAScope Reagents
|
|
|
|
PDX1 RNAscope probe |
ACD Bio |
Cat#43081 |
|
INS1 RNAscope probe |
ACD Bio |
Cat#313571-C4 |
| Human RNAscope 4-plex Positive Control Probes for RNAscope Multiplex Fluorescent Assay (POLR2A, PPIB, UBC and HPRT1
|
ACD Bio |
Cat#321801 |
| OPAL fluorophore 520 |
Akoya Biosciences |
Cat#FP1487001KT |
| OPAL fluorophore 620 |
Akoya Biosciences |
Cat#FP1495001KT |
| OPAL fluorophore 690 |
Akoya Biosciences |
Cat#FP1497001KT |
| OPAL Polaris fluorophore 780 |
Akoya Biosciences |
Cat#FP1501001KT |
| RNAscope 4-plex Multiplex Negative Control Probe |
ACD Bio |
Cat#321831 |
|
Bacterial and virus strains
|
|
Biological samples
|
|
|
| Human islets |
Integrated Islet Distribution Program (IIDP) |
RRIDS: SAMN17928660, SAMN25519947, SAMN25980818, SAMN13134368, SAMN13254972, SAMN13515839, SAMN13739565, SAMN12227196, SAMN17928660, SAMN25519947 |
|
Chemicals, peptides, and recombinant proteins
|
| Forskolin |
Sigma-Aldrich |
Cat#F3917 |
| Glucose |
Sigma-Aldrich |
Cat#G7528 |
| Lipofectamine 3000 |
Thermo Fisher Scientific |
Cat#L3000015 |
| Recombinant IL-1B |
Biolegend |
Cat#575102 |
| Recombinant mouse interleukin-1 receptor antagonist |
Sigma-Aldrich |
Cat#SRP6006 |
| Recombinant human interleukin-1 receptor antagonist |
MedChemExpress |
Cat#AMG-719 |
| TRI reagent |
Molecular Research |
Cat#NC9277980 |
| Collagenase from Clostridium histolyticum
|
Sigma-Aldrich |
Cat#C7657 |
| Tagment DNA Enzyme (TE) and Buffer (TD) |
Illumina |
Cat#FC-121–1030 |
| Formaldehyde |
Polysciences |
Cat#18814 |
| Glycine |
Fisher Scientific |
Cat#BP381–5 |
| DMSO |
Sigma |
Cat#D8418 |
| Sodium chloride |
Fischer Scientific |
Cat#BP35–10 |
| Ethylenediaminetetraacetic acid (EDTA) |
Lonza |
Cat#51234 |
| NP-40 |
Sigma |
Cat#NP40s |
| SDS |
Sigma |
Cat#L3771 |
| Triton X-100 |
Sigma |
Cat#X100 |
| Trypsin |
Fisher Scientific |
Cat#25300054 |
| Mini EDTA-free protease inhibitor cocktail |
Roche |
Cat#11836170001 |
| HALT protease and phosphatase inhibitors |
Thermo Fisher Scientific |
Cat#78444 |
| Anti-rabbit IgG dynabeads |
Thermo Fisher Scientific |
Cat#11204D |
| Streptavidin M280 dynabeads |
Thermo Fisher Scientific |
Cat#11205D |
| Penicillin-streptomycin |
Gibco |
Cat#15–140-122 |
| L-glutamine |
Fischer Scientific |
Cat#25–030-081 |
| Direct-zol miniprep columns |
Zymo Research |
Cat#R2052 |
| NEBNext Poly(A) mRNA magnetic isolation module |
New England Biolabs |
Cat#E7490S |
| NEBNext Ultra II directional RNA library kit |
New England Biolabs |
Cat#E7760 |
| NEBNext single cell/low input RNA library prep kit for Illumina |
New England Biolabs |
Cat#E6420S |
| Ampure XP reagent |
Beckman |
Cat#A63881 |
| MinElute PCR purification kit |
Qiagen |
Cat#28004 |
| Q5 High-Fidelity 2X master mix |
New England Biolabs |
Cat#M0492L |
| Di(N-succinimidyl) glutarate (DSG) |
Proteochem |
Cat#C1104 |
| Biocoll |
Millipore |
Cat#L6155 |
|
Critical commercial assays
|
| Insulin ELISA Assays |
Crystal Chem Inc |
Cat#90082 |
| C-peptide ELISA Assays |
Crystal Chem Inc |
Cat#90050 |
| NextSeq 500/550 High Output Kit v2.5 (75 Cycles) |
Illumina |
Cat#20024906 |
| NextSeq 2000 P3 Reagents (100 Cycles) |
Illumina |
Cat#20040559 |
| NE-PER Nuclear and Cytoplasmic Reagent Kit |
Thermo Fisher Scientific |
Cat#78835 |
|
Deposited data
|
| Sequence data, analyses, and resources related to the sequencing of human and mouse tissues and cells |
Gene Expression Omnibus |
GSE214678 |
|
Experimental models: Cell lines
|
| Beta-TC-6 cells |
American Type Culture Collection (ATCC) |
CRL-11506 |
| BMAL1 KO cells |
Dr. Joseph Bass, Northwestern University |
|
|
Experimental models: Organisms/strains
|
|
Pdx1+/− mice |
Dr. Roland Stein, Vanderbilt University |
|
|
Pdx1ΔAIV/− mice |
Dr. Roland Stein, Vanderbilt University |
|
|
PerLuc mice |
Dr. Joseph Takahashi, UT Southwestern |
|
|
Oligonucleotides
|
| Anti-Pdx1 siRNA |
ThermoFisher |
Cat#4390771 |
| Select Negative Control No. 1 siRNA |
ThermoFisher |
Cat#AM4611 |
| ATAC-seq indexing primers 1–12 92
|
Integrated DNA Technologies |
Custom order |
|
Recombinant DNA
|
|
Software and algorithms
|
| R (v4.1.2) |
The R Foundation |
|
| DESeq2 package (v1.36.0) |
Love, 201457
|
Bioconductor |
| Seurat package (v4.1.0) |
Satija, 201593
|
Bioconductor |
|
pathfindR (v2.3.0) |
Ulgen94
|
|
| Lme package (v1.1) |
DOI: 10.18637/jss.v067.i01
|
Bioconductor |
| Cell Ranger ATAC (v2.0.0) |
10X Genomics |
https://www.10xgenomics.com/software
|
| Cell Ranger (v6.1.2) |
10X Genomics |
https://www.10xgenomics.com/software
|
| ChIPseeker package (v1.31.3) |
Yu, 201595
|
Bioconductor |
| ChromVAR package (v1.16.0) |
Schep, 201727
|
Bioconductor |
| Cicero package (v1.3.5) |
Pliner, 201896
|
Bioconductor |
| STAR (v2.5.0) |
Dobin, 201397
|
https://github.com/alexdobin/STAR
|
| RSEM (v1.3.3) |
Li, 201198
|
https://github.com/deweylab/RSEM
|
| Prism (v9.0) |
GraphPad |
|
| HiC-Pro (v3.1.0) |
Servant 20187
|
https://github.com/nservant/HiC-Pro
|
| Juicer (v1.6) |
Durand, 20 1 699
|
https://github.com/aidenlab/juicer
|
| HiC-Explorer (v2.2) |
Ramirez, 2018100
|
https://github.com/deeptools/HiCExplorer
|
| FitHiChIP (v8.0) |
Bhattacharyya, 201989
|
https://github.com/ay-lab/FitHiChIP
|
| ClockLab Data Collection and Analysis System (v6.0) |
Actimetrics |
https://actimetrics.com
|
|
Other
|
| Islet snATAC-seq dataset |
Chiou, 20213
|
GSE160472, GSE160473, GSE163610
|
| Islet snRNA-seq dataset |
Xin, 201825
|
GSE114297 |
| R scripts and objects |
|
https://github.com/bjw032/PDX1_scATAC
|
