REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides, and Recombinant Proteins
Proteinase K	Merck	1.24568.0100
FM4-64	ThermoFisher	T3166
Tn5 transposase	Protein Expression Core Facility, EMBL	N/A
Pronase	Merck	P5147
Sodium thioglycolate	Merck	T0632
Critical Commercial Assays
NEBNext Ultra II DNA library preparation kit	NEB	E7645S
MirVana miRNA isolation kit	ThermoFisher	AM1560
TruSeq RNA Sample Preparation	Illumina	FC-122-1001
DIG RNA SP6/T7 labeling kit	Roche	11175025910
Rneasy mini kit	QIAGEN	74104
Superscript III First-Strand Synthesis SuperMix kit	ThermoFisher	18080-400
Deposited Data
scRNA-Seq of Phallusia mammillata from 2-cell to 16-cell stage	This paper	ArrayExpress E-MTAB-6506
scRNA-Seq of Phallusia mammillata from 32-cell to 64-cell stage	This paper	ArrayExpress E-MTAB-6508
Gene expression profiles during Phallusia mammillata embryogenesis	This paper	ArrayExpress E-MTAB-6528
Genome sequencing of Phallusia mammillata	This paper	ArrayExpress E-MTAB-6530
single cell RNA-Seq data of Ciona robusta embryos	Treen et al., 2018	GSE110588
Experimental Models: Organisms/Strains
Adult Phallusia mammillata	Roscoff Marine Station	N/A
Oligonucleotides
Primer: PH domain of human PLCD1 Forward: AATACGCGTAACTCGAGATGGACTCGGGCC GGGACTTCC	This paper	N/A
Primer: PH domain of human PLCD1 Reverse: CTAGTCGACGATGTTGAGCTCCTTCAGGAA GTTCTGC	This paper	N/A
Primers for in situ probes, see Table S3	This paper	N/A
Recombinant DNA
Genomic AHC0AAA267YK08 clone	Brozovic et al., 2018	N/A
Plasmid pRN3-MX	This paper	N/A
Plasmid pRN3-PH-Citrine	This paper	N/A
Plasmid pRN3-H2B-mCherry	This paper	N/A
Software and Algorithms
Python 2.7.5	Python Software Foundation	https://www.python.org
Numpy 1.7.1	N/A	http://numpy.org
Scipy 0.12.0	N/A	http://scipy.org
Velvet	Zerbino and Birney, 2008	https://github.com/dzerbino/velvet
Oases	Schulz et al., 2012	https://github.com/dzerbino/oases
BLAST	Altschul et al., 1990	https://blast.ncbi.nlm.nih.gov
Bowtie 1.0	Langmead et al., 2009	https://bio.sourceforge.io/
ImageJ	Schneider et al., 2012	https://imagej.nih.gov/ij/
ImageMagick	ImageMagick Studio LLC	https://imagemagick.org/index.php
Chimera	Pettersen et al., 2004	http://www.cgl.ucsf.edu/chimera
ilastik	Sommer et al., 2011	https://www.ilastik.org
tulip	Auber et al., 2016	https://sourceforge.net/projects/auber/files/tulip/tulip-4.9.0/
IMARIS v. 8.4.1	Bitplane	https://imaris.oxinst.com
MARS	Fernandez et al., 2010	https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fnmeth.1472
Amira v. 5.4.1 & v. 6.4.3	Thermo Scientific	https://thermofisher.com/amira-avizo
Blender	Blender Foundation	https://www.blender.org
MATLAB	Mathworks	https://www.mathworks.com/products/matlab
SCECTION	This paper	https://git.embl.de/neveu/morphoseq
Other
Resource website for the scRNA-Seq of P. mammillata embryos	This paper	http://Digitalembryo.org