Materials
Name | Company | Catalog Number | Comments |
1 kb Plus DNA Ladder | Invitrogen | 10787018 | |
100% Ethanol | |||
15 mL falcon tubes | |||
16% Formaldehyde Solution (w/v), Methanol-free | Thermo scientific | 28906 | |
5 mL tube | |||
5PRIME Phase Lock tubes | Quantabio | 2302820 | Phase lock gel - light |
AGANI needle 25 G | Terumo | AN*2516R1 | |
Agarose | |||
Bovine Serum Albumin | Sigma-Aldrich | A7030 | |
Bowtie | open source, available from https://bowtie-bio.sourceforge.net/index.shtml | ||
Branson sonifier 250 | Branson | Sonicator | |
Centrifuge | Eppendorf | 5430 R | With rotors for 15 mL and 1.5 mL tubes |
ChIP-grade antibody (here polyclonal H3K4me3 antibody) | Diagenode | C15410003 | |
Complete EDTA-free Protease Inhibitor Cocktail | Roche | 11873580001 | 2 tablets/mL water for 100x stock |
Cover glass | vwr | 48393 194 | |
Disposable Spatula | vwr | 80081-188 | |
DNA purification kit (here QIAGEN QIAquick PCR purification kit) | QIAGEN | 28104 | |
Dounce tissue grinder | Wheaton | tight pestle | |
Dulbecco's Phosphate Buffered Saline (DPBS) 1x | gibco | 14190-094 | |
Dynabeads Protein G | Thermo Fisher Scientific | 10004D | |
EDTA | Sigma-Aldrich | 3609 | |
EGTA | Sigma-Aldrich | 324626 | |
Electrophoresis system | |||
Ethidium bromide | |||
FASTQC v0.11.9 | software | ||
Gel Doc EZ Documentation System | Bio-Rad | 1708270 | Gel imaging system |
Glycine | Sigma-Aldrich | 50046 | |
Injekt-F Tuberculin syringe 1 mL | B. Braun | 9166017V | |
Linear acrylamide (5 mg/mL) | Invitrogen | AM9520 | |
Low-retention 1.5 mL tube | |||
Magnetic separation rack | for 1.5 mL tubes | ||
Microscope | |||
Microscope slide | |||
Model-based Analysis of ChIP-Seq (MACS) | open source | ||
Mortar and pestle, porcelain | |||
NanoDrop 2000c spectrophotometer | Thermo scientific | ND-2000C | |
N-lauroylsarcosine | Sigma-Aldrich | 61739 | |
Nuclease-free water | |||
Pasteur pipette | |||
Phenol:Chloroform:Isoamyl Alcohol Mixture (25:24:1) | Sigma-Aldrich | 77617 | |
Proteinase K (20 mg/mL) | Ambion | AM2546 | |
Purple Loading Dye 6x | New England BioLabs | B7024S | |
Qubit 2.0 Fluorometer | Invitrogen | ||
RNase Cocktail Enzyme Mix | Invitrogen | AM2286 | RNase A = 500 U/mL, RNase T1 = 20000 U/mL |
Sodium acetate | Sigma-Aldrich | S2889 | |
Sodium chloride | Sigma-Aldrich | S9888 | |
Sodium deoxycholate | Sigma-Aldrich | 30970 | |
SYBR Safe DNA Gel Stain | Invitrogen | S33102 | |
TAE buffer | |||
Thermomixer | Eppendorf | 5384000012 | |
Tris base | Sigma-Aldrich | 10708976001 | |
Triton X-100 solution | Sigma-Aldrich | 93443 | |
Trypan Blue Stain (0.4%) | Gibco | 15250-061 | Danger: may cause cancer. Suspected of damaging fertility or the unborn child |
Tube rotator SB3 | Stuart | ||
UltraPure SDS Solution, 10% | Invitrogen | 15553027 | |
Vacuum pump |
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