| Genetic reagent (Drosophila melanogaster) |
Cas9 |
Bloomington Drosophila Stock Center |
BDSC: 55821 |
y[1] M{GFP[E.3xP3]=vas-Cas9.RFP-}ZH-2A w[1118] |
| Genetic reagent (D. melanogaster) |
ΦC31 |
This lab |
N/A |
w[1], ΦC31 (y+); TM6, Tb, Hm/Sb |
| Genetic reagent (D. melanogaster) |
|
This lab |
N/A |
w[1]; TM6, Tb, Hm/Sb |
| Genetic reagent (D. melanogaster) |
Fub-1attP
|
This paper |
N/A |
Available from Paul Schedl laboratory in Princeton university. Contact pschedl@princeton.edu |
| Genetic reagent (D. melanogaster) |
Fab-7attP50
|
This lab |
N/A |
Available from Paul Schedl laboratory in Princeton university. Contact pschedl@princeton.edu |
| Genetic reagent (D. melanogaster) |
FLP |
Bloomington Drosophila Stock Center |
BDSC: 8727 |
P{w[+mC]=ovoFLP.R}M1A, w[*] |
| Genetic reagent (D. melanogaster) |
Cre |
Bloomington Drosophila Stock Center |
BDSC: 851 |
y[1] w[67c23] P{y[+mDint2]=Crey}1b; D[*]/TM3, Sb[1] |
| Antibody |
Anti- Abd-B (mouse monoclonal) |
Developmental Studies Hybridoma Bank |
1A2E9 |
IF(1:50) |
| Antibody |
Anti-Ubx (mouse monoclonal) |
Developmental Studies Hybridoma |
FP3.38 |
IF(1:50) |
| Antibody |
Anti-DsRed antibody (mouse monoclonal) |
Santa Cruz Biotechnology |
sc-390909 |
IF(1:50) |
| Antibody |
Anti-GFP antibody (rabbit polyclonal) |
Thermo Fisher Scientific |
A-11122 |
IF(1:500) |
| Antibody |
Anti-mouse Alexa Fluor 546 (goat polyclonal) |
Thermo Fisher Scientific |
A-11030 |
IF(1:500) |
| Antibody |
Anti-rabbit Alexa Fluor 488 (goat polyclonal) |
Thermo Fisher Scientific |
A-11008 |
IF(1:500) |
| Chemical compound, drug |
Paraformaldehyde 20% solution, EM Grade |
Electron Microscopy Sciences |
15713S |
|
| Chemical compound, drug |
Formaldehyde, 16%, methanol free, Ultra Pure |
Polysciences Inc |
18814-10 |
|
| Chemical compound, drug |
Phosphate-buffered saline (10×) pH 7.4, RNase-free |
Thermo Fisher |
AM9624 |
|
| Chemical compound, drug |
Tween 20 |
Sigma |
P1379 |
|
| Chemical compound, drug |
Triton X-100 |
Bio-Rad |
161-0407 |
|
| Chemical compound, drug |
Tris base |
Sigma |
11814273001 |
|
| Chemical compound, drug |
Methanol |
Fisher Chemical |
203403 |
|
| Chemical compound, drug |
SSC, 20× |
Thermo Fisher Scientific |
15557044 |
|
| Chemical compound, drug |
Formamide |
Thermo Fisher Scientific |
17899 |
|
| Chemical compound, drug |
Dextran sulfate |
Sigma |
D8906 |
|
| Chemical compound, drug |
Salmon Sperm DNA |
Thermo Fisher Scientific |
AM9680 |
|
| Chemical compound, drug |
Ribonucleoside Vanadyl Complex |
NEB |
S1402S |
|
| Chemical compound, drug |
Nuclease-free BSA |
Sigma |
126609 |
|
| Chemical compound, drug |
Triethylammonium acetate |
Sigma |
625718 |
|
| Chemical compound, drug |
dGTP (100 MM) |
VWR |
76510-208 |
|
| Chemical compound, drug |
dTTP (100 MM) |
VWR |
76510-224 |
|
| Chemical compound, drug |
Lonza NuSieve 3:1 Agarose |
Thermo Fisher Scientific |
BMA50090 |
|
| Chemical compound, drug |
T4 DNA ligase |
NEB |
M0202L |
|
| Chemical compound, drug |
Biotin-11-dCTP |
Jen Bioscience |
NU-809-BIOX |
|
| Chemical compound, drug |
Biotin-14-dATP |
Jen Bioscience |
NU-835-BIO14 |
|
| Chemical compound, drug |
Qubit dsDNA HS Assay Kit |
Life Technologies Corporation |
Q32851 |
|
| Chemical compound, drug |
Phase Lock Gel, QuantaBio - 2302830, Phase Lock Gel Heavy |
VMR |
10847-802 |
|
| Chemical compound, drug |
NEBNext Ultra II DNA Library Prep Kit for Illumina |
NEB |
E7645S |
|
| Chemical compound, drug |
Ampure Xp 5 ml Kit |
Thermo Fisher Scientific |
NC9959336 |
|
| Chemical compound, drug |
Hifi Hotstart Ready Mix |
Thermo Fisher Scientific |
501965217 |
|
| Chemical compound, drug |
Dynabeads MyOne Streptavidin C1 |
Life Technologies Corporation |
65001 |
|
| Chemical compound, drug |
cOmplete, EDTA-free Protease Inhibitor Cocktail |
Sigma |
11873580001 |
|
| Chemical compound, drug |
N,N-Dimethylformamide |
Sigma |
227056 |
|
| Chemical compound, drug |
Potassium acetate solution |
Sigma |
95843 |
|
| Chemical compound, drug |
DSG (disuccinimidyl glutarate) |
Thermo Fisher Scientific |
PI20593 |
|
| Chemical compound, drug |
T4 Polynucleotide Kinase – 500 units |
NEB |
M0201S |
|
| Chemical compound, drug |
DNA Polymerase I, Large (Klenow) Fragment – 1000 units |
NEB |
M0210L |
|
| Chemical compound, drug |
End-it DNA End Repair Kit |
Thermo Fisher Scientific |
NC0105678 |
|
| Chemical compound, drug |
Proteinase K recomb. 100 mg |
Sigma |
3115879001 |
|
| Chemical compound, drug |
Nuclease Micrococcal (s7) |
Thermo Fisher Scientific |
NC9391488 |
|
| Chemical compound, drug |
EGS (ethylene glycol bis(succinimidyl succinate)) |
Thermo Fisher Scientific |
PI21565 |
|
| Sequence-based reagent |
Fub-1 sense probe set |
Biosearch Technologies |
N/A |
|
| Sequence-based reagent |
Fub-1 antisense probe set |
Biosearch Technologies |
N/A |
|
| Software, algorithm |
Fiji (ImageJ) |
Schindelin et al., 2012
|
|
fiji.sc |
| Software, algorithm |
NIS element |
Nikon |
|
https://www.microscope.healthcare.nikon.com/products/software/nis-elements/
|
| Software, algorithm |
GraphPad Prism 8 |
GraphPad Software |
|
https://www.graphpad.com
|
| Software, algorithm |
HiGlass |
Kerpedjiev et al., 2018
|
|
http://higlass.io/
|
| Software, algorithm |
bwa |
Li and Durbin, 2009
|
|
https://bio-bwa.sourceforge.net/
|
| Software, algorithm |
samtools |
Github/open source |
|
https://samtools.github.io
|
| Software, algorithm |
pairsamtools |
Github/open source; Goloborodko et al., 2023
|
|
https://github.com/open2c/pairtools
|
| Software, algorithm |
pairix |
Github/open source; Lee et al., 2021
|
|
https://github.com/4dn-dcic/pairix
|
| Software, algorithm |
cooler |
Abdennur et al., 2023
|
|
https://github.com/open2c/cooler
|
| Software, algorithm |
Miniconda |
Anaconda |
|
https://docs.conda.io/en/latest/miniconda.html
|
| Software, algorithm |
Snakemake |
Github/open source |
|
https://snakemake.github.io
|
