Online Table 2 Materials and reagents used in this study.
Protocol Section | Reagents | Manufacture | Identifier | Volume/Concentration | |
|---|---|---|---|---|---|
Cell Growth and Expansion | RPMI 1640 (with 25 mM HEPES) | Thermo Fisher Scientific | 22400089 | ||
Iscove’s IMDM | Thermo Fisher Scientific | 12440053 | |||
L-glutamine | Thermo Fisher Scientific | 25030081 | 2 mM | ||
Hyclone Fetal Bovine Serum (FBS) | Fisher Scientific | SH3007.13 | 10% (RMPI) | ||
20% (IMDM) | |||||
Antibiotic/antimycotic | Thermo Fisher Scientific | 15240062 | 1.0% | ||
Insulin/Transferrin/Selenium (ITS) | Corning Life Science | 354351 | 0.1% (IMDM) | ||
Immunobltoing | Cell Lysis Buffer (1 mL) | Cell Lysis Buffer | Cell Signaling | 9803 | 100 μL |
PMSF | Cell Signaling | 8553S | 20 μl (100 mM) | ||
Phosphatase Inhibitor Cocktail 2 | Sigma Aldrich | P5726 | 10 μL | ||
Phosphatase Inhibitor Cocktail 3 | Sigma Aldrich | P0044 | 10 μL | ||
PBS | Gibco | 14190-136 | 860 μL | ||
4X Laemmli Sample Buffer | BioRad | 1610747 | |||
Pierce BCA Protein Assay Kit | Thermo Scientific | 23225 | |||
4–15% Criterion TGX Precast Midi Protein Gel | BioRad | 5671085 | |||
N-MYC | Cell Signaling | 9405 S | 1:1000 | ||
MYC | Cell Signaling | 5605 | 1:800 | ||
B-Actin | Cell Signaling | 4976 S | 1:5000 | ||
Rabbit Secondary | Millipore | AP132P | 1:2000-1:5000 | ||
ChIP-Seq | Formaldehyde Solution | 37% Formaldehyde | Sigma Aldrich | F8775 | 11% |
5.0 M NaCl | Sigma Aldrich | S5150 | 0.1 M | ||
0.5 EDTA (pH 8.0) | Invitrogen | 15575-038 | 1 mM | ||
1.0 M HEPES (pH 7.9) | Gibco | 15630-080 | 50 mM | ||
Nuclease-free H2O | Ambion | AM9937 | |||
Glycine Solution | Glycine (mw 75) | Sigma Aldrich | G7403 | 2.5 M | |
Nuclease-free H2O | Ambion | AM9937 | |||
Other Cell Fixation Reagents: | PMSF | Cell Signaling | 8553 S | 100 mM | |
Antibodies | N-Myc | Active Motif | #61185 | 6 μL | |
c-Myc | Santa Cruz N262 | #sc-764 | 20 μl | ||
H3K4me1 | Active Motif | #39297 | 5 μl | ||
H3K4me3 | Active Motif | #39159 | 3 μl | ||
H3K27Ac | Active Motif | #39133 | 4 μg | ||
HeK27me3 | Millipore | #07-449 | 4 μg | ||
H3K4me1 | Active Motif | #39297 | 5 μl | ||
FA Lysis Buffer | 1.0 M HEPES (pH 7.5) | Gibco | 15630-080 | 50 mM | |
NaCl | Sigma | S5150 | 140 mM | ||
EDTA (pH 8.0) | Invitrogen | 15575-038 | 1 mM | ||
Triton-X-100 | Sigma | 9002-93-1 | 0.10% | ||
SDS | Invitrogen | 15553-035 | 0.10% | ||
Sodium deoxycholate | VWR | 97062-028 | 0.10% | ||
Protease Inhibitors | Thermo Scientific | 88666 | |||
DTT | Fisher | CAS 3483-12-3 | 1 mM | ||
ChIP Wash Buffer | Tris-HCl (pH 8.0) | Invitrogen | 15568-025 | 20 mM | |
NaCl | Sigma | S5150 | 150 mM | ||
EDTA (pH 8.0) | Invitrogen | 15575-038 | 2 mM | ||
Triton-X-100 | Sigma | 9002-93-1 | 1.00% | ||
SDS | Invitrogen | 15553-035 | 0.10% | ||
Sodium deoxycholate | VWR | 97062-028 | 0.10% | ||
Final Wash Buffer | Tris-HCl (pH 8.0) | Invitrogen | 15568-025 | 20 mM | |
NaCl | Sigma | S5150 | 500 mM | ||
EDTA (pH 8.0) | Invitrogen | 15575-038 | 2 mM | ||
Triton-X-100 | Sigma | 9002-93-1 | 1.00% | ||
SDS | Invitrogen | 15553-035 | 0.10% | ||
Tris-HCl (pH 8.0) | Invitrogen | 15568-025 | 20 mM | ||
Other ChIP-Seq Reagents | NEB Ultra Kit | New England Biosciences | E7370S | ||
Protein A/G Beads | Thermo Scientific | 26162 | |||
ATAC-Seq | ATAC-Seq Lysis Buffer | Tris-HCl (pH 7.4) | Invitrogen | 15567027 | 10 mM |
NaCl | Sigma | S5150 | 10 mM | ||
MgCl2 | Fisher | 7791-18-6 | 3 mM | ||
lgepal CA-630, molecular biology grade | Sigma | I8896 | 0.10% | ||
Other ATAC-Seq Reagents | 1X Phosphate Buffered Saline (PBS) | Gibco | 14190-136 | 10 mM | |
TDB | Illumina | FC-121-1030 (2X reaction buffer from Nextera Kit) | 2X | ||
TDE1 | Illumina | FC-121-30 (Nextera Tn5 Transposase from Nextera Kit) | |||
Nuclease-free H2O | Ambion | AM9937 | |||
NEBNext High-Fidelity 2X PCR Master Mix | NEB | M0541 | |||
10,000X SYBR Green | Invitrogen | S-7563 | 9X | ||
MinElute PCR Purification Kit | Qiagen | 28104 | |||
AMPure XP Beads | Beckman Coulter | A63880 | |||
SPRI Beads | Beckman Coulter | B23317 |
