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. 2019 Jan 15;8:e39356. doi: 10.7554/eLife.39356

Key resources table.

Reagent type. Designation. Source (public). Identifiers. Additional information.
Transfected
construct
(Xenopus laevis)		 ath5::GAP-eGFP Das et al., 2003,
PMID: 12597858;
Zolessi et al., 2006,
PMID: 17147778		 ZFIN ID:
ZDB-TGCONSTRCT-070129–1		 Membrane-tagged GFP
under control of ath5 (atoh7)
promoter; pCS2 + vector
Biological sample
(Xenopus laevis)		 Xenopus laevis National Xenopus Resource Cat #:
NXR_0.0031; RRID:SCR_013731 		Wild-type strain Xla.
NXR-WTNXR
Antibody Rabbit polyclonal
anti-phospho-Histon
H3 (sER10)		 EMD Millipore Cat #: 06–570;
RRID:AB_310177 		IHC (1:1000)
Antibody Goat anti-rabbit
Alexa Fluor 594		 Abcam Cat #: AB150084;
RRID:AB_2734147 		IHC (1:500)
Chemical
compound, drug		 BI2536 MedChem Express Cat#: HY-50698 50 µM
Chemical
compound, drug		 Hydroxyurea Sigma Cat#: H8627-5G 20 mM
Chemical
compound, drug		 Aphidicolin Sigma Cat#: A0781-5MG 150 µM
Chemical
compound, drug		 1M Sodium
hydroxide		 Sigma fabrication of
polyacrylamide substrates
Chemical
compound, drug		 (3-aminopropyl)
trimethoxysilane		 Sigma-Aldrich Cat#: 281778–100 ML fabrication of
polyacrylamide substrates
Chemical
compound, drug		 glutaraldehyde Sigma-Aldrich Cat#: G6257-1L fabrication of
polyacrylamide substrates
Chemical
compound, drug		 40% w/v acrylamide
solution		 Sigma-Aldrich Cat#: A4058-100ML fabrication of
polyacrylamide substrates
Chemical
compound, drug		 2% bis-acrylamide Fisher Scientific Cat#: BP1404-250 fabrication of
polyacrylamide substrates
Chemical
compound, drug		 ammonium persulfate Sigma Cat#: 215589 fabrication of
polyacrylamide substrates
Chemical
compound, drug		 N,N,N',N'-tetramethylethylenediamine ThermoFisher Cat#: 15524–010 fabrication of
polyacrylamide substrates
Chemical
compound, drug		 hydrazine hydrate Sigma-Aldrich Cat#: 225819–500 mL fabrication of
polyacrylamide substrates
Chemical
compound, drug		 5% acetic acid ACROS Organics Cat#: 10041250 fabrication of
polyacrylamide substrates
Chemical
compound, drug		 Poly-D-lysine Sigma-Aldrich Cat#: P6407-5MG 10 µg/ml
Chemical
compound, drug		 laminin Sigma-Aldrich Cat#: L2020-1MG 5 µg/ml
Software,
algorithm		 Fiji Fiji is Just ImageJ
(https://fiji.sc)		 RRID:SCR_002285
Software,
algorithm		 Adobe Illustrator Adobe Illustrator RRID:SCR_010279
Software,
algorithm		 MATLAB MATLAB RRID:SCR_001622 Codes used for Sholl analysis post-processing, OT elongation, motorized stage control, processing of AFM raw data, mapping of stiffness maps onto brains and OT and local tissue stiffness gradient calculations can be found at https://github.com/FranzeLab/AFM-data-analysis-and-processing
(Franze, 2018a), https://github.com/FranzeLab/Image-processing-and-analysis (Franze, 2018b) and https://github.com/FranzeLab/Instrument-Control (Franze, 2018c; copies archived at https://github.com/elifesciences-publications/Image-processing-and-analysis,https://github.com/elifesciences-publications/Instrument-Control and https://github.com/elifesciences-publications/AFM-data-analysis-and-processing).
Other 4,6-diamidino-2-
phenylindole (DAPI)		 Sigma-Aldrich Cat#: D9542- 5 mg 1 µg/ml
Other Arrow-TL1 Tipless
silicon cantilevers		 NanoWorld
Innovative
technologies		 Manufacturer's ID:
ARROW-TL1-50		 Cantilevers for AFM-based
stiffness measurements
Other 37.28 µm
spherical polysterene
beads		 microParticles
GmbH		 Cat#: PS-R-37.0 Spherical probes attached
to AFM cantilevers
Other Rain-X Shell Car Care
International Ltd,
UK		 Model #: 800002250 fabrication of
polyacrylamide substrates
Other CellHesion-200
AFM head		 JPK Instruments Atomic force microscope
Other PetriDish Heater JPK Instruments Maintaining constant
temperature for time-lapse
AFM experiments