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7 protocols using t4661

1

Lactate Dehydrogenase Cytotoxicity Assay

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EpiDerm™ cell media were collected from flavor chemical and ECEAR treatments and immediately assayed using the OPS Diagnostics Lactate Dehydrogenase Protocol. Tris-HCl (Sigma-Aldrich, T-3253) and Tris-base (Sigma-Aldrich, T4661) were combined to make TRIS, pH 8. Iodonitrotetrazolium chloride (INT, Sigma I-8377) dissolved in DMSO (Sigma D-8779), phenazine methosulfate (PMS, Sigma P-9625), nicotinamide adenine dinucleotide (NAD, Sigma N-0632), and lithium lactate (Sigma L-1500) were prepared before use and stored at −20°C. 50 μL of 100mM TRIS were added to 50 μl of 50 mM lithium lactate and 50 μl of PMS, INT, NAD. 50 μl of sample were added to each well and after 5 minutes, the absorbance was read on a Synergy™ HTX Multi-Mode Microplate Reader (BioTek, VT). The cytotoxicity was calculated:
Abs(x)Abs(NegativeCN)Abs(PositiveCN)Abs(NegativeCN)x100
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2

Isolating Nuclei from HeLa S3 Cells

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HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (ThermoFisher Scientific, 10569010) supplemented with 10% fetal bovine serum (ThermoFisher Scientific, 16000044) and 1% penicillin-streptomycin (ThermoFisher Scientific, 10378016) at 37 °C with 5% CO2. Cells were not authenticated nor tested for mycoplasma. To prepare nuclei, HeLa S3 cells were harvested by centrifugation, washed with PBS (ThermoFisher Scientific, 10010–23) and counted using BioRad TC20 cell counter. The cells were then resuspended in cold Nuclei Permeabilization Buffer (NPB: 10 mM Tris-HCl pH 7.4 [Sigma, T4661], 10 mM NaCl [Sigma, S7653], 3 mM MgCl2 [Sigma, 63069], 1X Protease Inhibitor [Roche, 05056489001], 0.5 U/µL RNase OUT [Invitrogen, 10777–019] and 0.5 U/µL SUPERase Inhibitor [Invitrogen, AM2694]) with 0.1% IGEPAL CA-630 (Sigma, I8896) and centrifuged for 10 min at 1,000 g, 4 °C and proceed to Paired-Tag experiments.
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3

Generation of Barcoded Tn5 Transposomes

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To generate barcoded Tn5 transposomes, barcoded DNA adaptors oligos were annealed to a common pMENTs oligo (Supplementary Tables 1 and 2) in a thermocycler with the following program: 95 °C for 5min, slowly cooled to 10 °C with a temperature ramp of −0.1 °C/s. The transposons (1μL, 50 μM) were then mixed with 6 μL unloaded transposase Tn5 (0.5 mg/mL), mixed by brief vortex and quickly spin-down, incubated at room temperature for 30 min. 63 μL storage buffer (50% Glycerol [Sigma, G6279], 50 mM Tris-HCl pH 7.4 [Sigma, T4661], 100 mM NaCl [Sigma, S7653], 1 Mm DTT [Sigma, D9779]) was then added and the loaded transposases can be stored at −20 °C for up to 6 months.
To generate DNA barcoded plates, 6 μL 100 μM barcoded oligos (Supplementary Table 2) were distributed to 96-well plates. 44 μL 12.5 μM Linker-R02, Linker-R03 and Linker-R04 oligos (Supplementary Table 1) were then added to each well of the 96-well plates containing corresponding the barcoded oligos. The plates were then sealed and annealed in a thermocycler with the following program: 95 °C for 5 min, slowly cooled to 20 °C with a temperature ramp of −0.1 °C/s.
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4

Purification and Characterization of Active MMP1 from E. coli

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Active MMP1 was purified as described in a previous publication [39 (link)]. Briefly, the cDNA sequence of MMP1 was optimized for expression in E. coli and inserted into pET-21b (+) vector between NdeI (N-terminal) and HindIII (C-terminal) restriction sites. The plasmid was transformed into Rosetta (DE3) pLysS competent cells (Novagen, 70956). The cells were cultured in Luria Broth media (Sigma, L3022) to reach the optical density, OD600 = 0.1 (pH 7.0) at 37°C at 250 rpm in presence of chloramphenicol and ampicillin at the final concentrations of 34 μg/μl and 100 μg/μl respectively. The cells were induced for 5 hr with 1 mM Isopropyl β-D-1-thiogalactopyranoside (IPTG) and harvested after centrifugation. 1 g of the centrifuged cells was reconstituted in 7 ml of lysis buffer (pH 9.0) containing 50 mM Tris base (Sigma, T4661), 100 mM NaCl (Sigma, S9888), 200 μM ZnCl2 (Sigma, 208086), 400 μM CaCl2 (Sigma, 746495), freshly prepared 1% Triton X-100 (Sigma, T8787), 0.1 mg/ml trypsin (Worthington, TPCK-treated and irradiated, LS003750), and 1 mg/ml lysozyme (Sigma, L6878). The reconstituted cells were incubated for 18 hr at 37°C at 250 rpm and centrifuged to collect the supernatant, followed by centrifugation using 30 kD cut-off filters. MMP1 was quantified using Bradford assay and analyzed by SDS PAGE.
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5

Cell Nuclei Preparation and Mixing for Paired-seq

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HEK293T (human, ATCC CRL-11268), HepG2 (human, ATCC HB-8065) and NIH/3T3 (murine, ATCC CRL-1658) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific, 10569010) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, 16000044) and 1% penicillin–streptomycin (Thermo Fisher Scientific, 10378016) at 37 °C with 5% CO2. Cells were not authenticated nor tested for mycoplasma. To prepare nuclei, HepG2 and 3T3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific, 10010-23) and counted using BioRad TC20 cell counter. The percentage of live cells in the samples were higher than 95%. The cells were then resuspended in cold Lysis Buffer (10 mM Tris-HCl pH 7.4 [Sigma, T4661], 10 mM NaCl [Sigma, S7653], 3 mM MgCl2 [Sigma, 63069], 0.1% IGEPAL CA-630 [Sigma, I8896]) and centrifuged for 15 min at 600 g, 4 °C. For the species mixing experiment, nuclei were then washed with PBS and resuspended, counted using BioRad TC20 cell counter. HepG2, HEK293T and 3T3 nuclei were then mixed in equal proportions and applied to Paired-seq.
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6

Isolating Nuclei from HeLa S3 Cells

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HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (ThermoFisher Scientific, 10569010) supplemented with 10% fetal bovine serum (ThermoFisher Scientific, 16000044) and 1% penicillin-streptomycin (ThermoFisher Scientific, 10378016) at 37 °C with 5% CO2. Cells were not authenticated nor tested for mycoplasma. To prepare nuclei, HeLa S3 cells were harvested by centrifugation, washed with PBS (ThermoFisher Scientific, 10010–23) and counted using BioRad TC20 cell counter. The cells were then resuspended in cold Nuclei Permeabilization Buffer (NPB: 10 mM Tris-HCl pH 7.4 [Sigma, T4661], 10 mM NaCl [Sigma, S7653], 3 mM MgCl2 [Sigma, 63069], 1X Protease Inhibitor [Roche, 05056489001], 0.5 U/µL RNase OUT [Invitrogen, 10777–019] and 0.5 U/µL SUPERase Inhibitor [Invitrogen, AM2694]) with 0.1% IGEPAL CA-630 (Sigma, I8896) and centrifuged for 10 min at 1,000 g, 4 °C and proceed to Paired-Tag experiments.
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7

O-PAD-ELISA: Paper-Based Assay Design

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The O-PAD for ELISA (O-ELISA) was designed on Whatman qualitative filter paper No. 1 and patterned using a wax printer (Xerox Phaser 8650N color printer, Norwalk, CT, USA). Four wings were fashioned to house ELISA reagent loading zones for pre-loading, and the central area was designed and reserved as a testing zone for sample loading. After heating at 105 °C for 3 min, the melted wax wicked through the paper to create hydrophobic barrier wells in the paper. Reagents were then pre-loaded into reagent zone barrier wells. These reagents included the following: (1) 2 µL of blocking buffer (5% (w/v) bovine serum albumin (BSA) (Sigma, SI-A7906, St. Louis, MO, USA) in PBS (Corning, 21-040-CM, Corning, NY, USA); (2) 2 µL solution of alkaline phosphatase (ALP)-conjugated detection antibody (Cell signaling, #7054, Danvers, MA, USA) (20 µg/mL, 0.01% (v/v) Tween-20 (Sigma, P9416, St. Louis, MO, USA); and (3) 2 µL BCIP/NBT substrate (13.4 mM BCIP (Sigma, B6274), 9 mM NBT (Sigma, N5514), 25 mM MgCl2 (Sigma, M8266), 500 mM NaCl (Sigma, S7653) in 500 mM Tris buffer pH 9.5 (Sigma, T4661). After loading each reagent, the device was placed under ambient conditions for 5 to 10 min until the reagents dried.
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