KEY RESOURCES TABLE

REAGENT or RESOURCE		SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Tubb3		Abcam	Cat# AB18207 RRID:AB_444319
Chicken anti-mCherry		EMD Millipore	Cat#AB356481
Goat anti-Ass1		Abcam	Cat# ab77590 RRID:AB_2060467
Rabbit anti-Celsr3		Sigma-Aldrich	Cat# SAB4500707–100UG RRID:AB_10744051
Rabbit anti-Uchl1		Cell Signaling	Cat#13179T RRID:AB_2798141
Rabbit anti-ASL		Abcam	Cat# ab97370 RRID:AB_10680261
Rabbit anti-GRP		Abcam	Cat# ab22623 RRID:AB_447204
Rabbit anti-Prph		Abcam	Cat# ab4666 RRID:AB_449340
Goat anti-Phox2b		Novus Biologicals	Cat#AF4940
Mm-Calca		ACDBio	Cat#417961
Mm-Calcb		ACDBio	Cat#425511
Mm-Cck		ACDBio	Cat#402271
Mm-Chat-C2		ACDBio	Cat#408731-C2
Mm-GRP		ACDBio	Cat#317861-C2
Mm-Htr4		ACDBio	Cat#408241
Mm-Lgr5		ACDBio	Cat#312171
Mm-Nmu		ACDBio	Cat#446831
Mm-Nog		ACDBio	Cat#467391
Mm-Nos1-C3		ACDBio	Cat#437651-C3
Mm-Piezo1		ACDBio	Cat#500511
Mm-Piezo2-C3		ACDBio	Cat#400191-C3
Mm-Sst-C3		ACDBio	Cat#404631-C3
Mm-Tph2-C2		ACDBio	Cat#318691-C2
Mm-Vip/Mm-Vip-C2		ACDBio	Cat#415961/415961-C2
Hs-ANO1-C2		ACDBio	Cat#349021-C2
Hs-CHAT/Hs-CHAT-C2		ACDBio	Cat#450671/450671-C2
Hs-DSCAM		ACDBio	Cat#
Hs- GUCY1A3		ACDBio	Cat#425831
Hs-IL7		ACDBio	Cat#424251
Hs-IL12A		ACDBio	Cat#402061
Hs-KIT-C3		ACDBio	Cat#606401-C3
Hs-NOS1-C2		ACDBio	Cat#506551-C2
Hs-RET		ACDBio	Cat#424871
Hs-GRP		ACDBio	Cat#465261
Hs-SCN3A		ACDBio	Cat#460121
Biological Samples
Human cancer-proximal colon tissue from resections		Dana Farber Cancer Institute, Boston (IRB 03–189; ORSP 3490); Massachusetts General Hospital, Boston (IRB 02–240; ORSP 1702)	Table S1
Chemicals, Peptides, and Recombinant Proteins
CHAPS, Molecular Biology Grade		EMD Millipore	Cat#220201–1GM
Nonidet™ P40 Substitute, Ultrapure, Affymetrix/USB		Fisher Scientific	Cat#AAJ19628AP
Tween®-20 Solution, 10%		Teknova	VWR-100216–360
Triton X-100		Sigma-Aldrich	Cat#T8787–100ML
Digitonin		Promega	Cat#G9441
Hexylene Glycol		Sigma-Aldrich	Cat#112100–500GT
Tricine Buffer, Ultra Pure Grade		VWR	Cat#E170–100G
HEPES, 1M Solution, pH 7.3, Molecular Biology Grade, Ultrapure		Fisher Scientific	Cat# AAJ16924AE
Tris (1 M), pH 8.0, Rnase-Free		Thermo Fisher Scientific	Cat#AM9855G
Sodium Chloride Solution		Sigma-Aldrich	Cat#S6546–1L
CACL2 1M ST BIOTECH GRD		VWR	Cat#97062–820
Magnesium Chloride Solution		Sigma-Aldrich	Cat#M1028–10X1ML
Potassium Chloride Solution		Sigma-Aldrich	Cat#60142–100ML-F
Spermidine (1g)		Sigma-Aldrich	Cat#S2626–1G
Spermine (1g)		Sigma-Aldrich	Cat#S3256–1G
BSA, Molecular Biology Grade		New England Biolabs	Cat#B9000S
Sucrose, RNase & DNase Free, Ultra Pure Grade		VWR	Cat#97061–432
cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail		Sigma-Aldrich	Cat#11836170001
Cyclohexamide		Cell Signaling Technology	Cat#2112S
Cytochalasin D		Sigma-Aldrich	Cat#C2618–200UL
Recombinant RNase Inhibitor		Takara	Cat#2313B
Magnesium Acetate Solution		Sigma-Aldrich	63052–100ML
B-Mercaptoethanol		Sigma-Aldrich	Cat#M3148–100ML
Buffer TCL (125 mL)		Qiagen	Cat#1031576
Deoxynucleotide (dNTP) Solution Mix		New England Biolabs	Cat#N0447L
Maxima H Minus Reverse Transcriptase (200 U/uL)		Thermo Fisher Scientific	Cat#EP0753
KAPA HiFi HotStart ReadyMix PCR Kit		Roche	Cat#KK2602
tousimis® FORMALDEHYDE 20%		tousimis	Cat#1008A
TSA Plus Cyanine 5 and Flourescein System		PerkinElmer	Cat#NEL754001KT
TSA Plus Cyanine 3 Evaluation Kit		PerkinElmer	Cat#NEL744E001KT
Pierce™ 20X TBS Tween™ 20 Buffer		Thermo Fisher Scientific	Cat#28360
DAPI		Sigma-Aldrich	Cat#D9542–10MG
Tissue-Tek O.C.T. compound 4583		VWR	Cat#25608–930
Vybrant DyeCycle Ruby Stain		Thermo Fisher Scientific	Cat#V-10309
CAS-Block™ Histochemical Reagent		Thermo Fisher Scientific	Cat#008120
RNAscope® Probe Diluent		ACD	Cat#300041
Critical Commercial Assays
Agencourt RNAClean (RNA SPRI beads)		Beckman Coulter	Cat#A63987
Nuclei EZ Prep		Sigma-Aldrich	Cat#NUC101–1KT
AMPureXP SPRI (DNA SPRI beads)		Beckman Coulter	Cat#A63881
Nextera XT DNA Library Preparation Kit		Illumina	Cat#FC-131–1096
NextSeq 500 high output kit V2, 75 cycles		Illumina	Cat#FC-404–2005
RNAscope® Fluorescent Multiplex Reagent Kit		ACD	Cat#320850
10X Chromium Single Cell 3’ Kit		10X Genomics	Cat#120237
Deposited Data
Genome Reference Consortium Mouse Build GRCm38		Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/
Genome References Consortium Human Build GRCh37		Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/
TcoF-DB v2 human transcription factors		Schmeier et al., 2016	http://compbio.massey.ac.nz/apps/tcof/home/
PRRDB human pattern recognition receptors		Lata et al., 2008	http://crdd.osdd.net/raghava/prrdb/
FANTOM5 receptor-ligand database		Ramilowski et al., 2015	http://fantom.gsc.riken.jp/5
Mouse SS2 – FASTQ files and processed data		This paper	Single cell portal accession SCP1038 (https://portals.broadinstitute.org/single_cell)
Mouse 10X – FASTQ files and processed data		This paper	Single cell portal accession SCP1038 (https://portals.broadinstitute.org/single_cell)
Human 10X - FASTQ files		This paper	Broad DUOS project “ColonENS-RegevXavier-CRCAdjacentNormal-Broad-snRNASeq-UnsortedCells” (https://duos.broadinstitute.org)
Human 10X – processed data		This paper	Single cell portal accession SCP1038 (https://portals.broadinstitute.org/single_cell)
Experimental Models: Organisms/Strains
C57BL/6J		The Jackson Laboratory	Cat#000664 RRID:IMSR_JAX:000664
B6;CBA-Tg(Sox10-cre)1Wdr/J		The Jackson Laboratory	Cat#025807 RRID:IMSR_JAX:025807
129S4.Cg-E2f1Tg(Wnt1-cre)2Sor/J		The Jackson Laboratory	Cat#022137 RRID:IMSR_JAX:022137
B6;129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J		The Jackson Laboratory	Cat#021039 RRID:IMSR_JAX:021039
Tg(Uchl1-HIST2H2BE/mCherry/EGFP*)FSout/J		The Jackson Laboratory	Cat#016981 RRID:IMSR_JAX:016981
Oligonucleotides
Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 mM) 5’ -AAGCAGTGGTATCAACGCAGAGTACT(30)VN-3’		IDT	N/A
SMARTER TSO (with LNA) 5’ -AAGCAGTGGTATCAACGCAGAGTACrGrG+G-3’		Exiqon	N/A
PCR oligonucleotide primer 5’ -AAGCAGTGGTATCAACGCAGAGT-3’		IDT	N/A
Recombinant DNA
Software and Algorithms
CellRanger v2.0		10X Genomics	https://github.com/10XGenomics/cellranger
sva (R package)		Leek et al., 2014	https://www.bioconductor.org/packages/devel/bioc/html/sva.html
Infomap clustering algorithm		Rosvall et al., 2008	http://igraph.org/
Barnes-Hut t-SNE algorithm		van der Maaten et al., 2014	https://cran.r-project.org/web/packages/Rtsne/
Scanpy		Wolf et al., 2018	https://github.com/theislab/scanpy
MAST		Finak et al., 2015	https://github.com/RGLab/MAST
Rtsne		CRAN	https://cran.r-project.org/web/packages/Rtsne/
PhenoGraph		Levine et al., 2015	https://github.com/jacoblevine/PhenoGraph
MAGIC		van Dijk et al., 2018	https://github.com/KrishnaswamyLab/MAGIC
nlme (R package)		CRAN	https://cran.r-project.org/web/packages/nlme/index.html
rsvd (R package)		CRAN	https://cran.r-project.org/web/packages/rsvd/index.html
Seurat (R toolkit)		Butler et al., 2018	https://satijalab.org/seurat
Analysis code		This paper	https://github.com/klarman-cell-observatory/ens_atlas
REAGENT or RESOURCE	SOURCE		IDENTIFIER
Antibodies
Rabbit monoclonal anti-Snail	Cell Signaling Technology		Cat#3879S; RRID: AB_2255011
Mouse monoclonal anti-Tubulin (clone DM1A)	Sigma-Aldrich		Cat#T9026; RRID: AB_477593
Rabbit polyclonal anti-BMAL1	This paper		N/A
Bacterial and Virus Strains
pAAV-hSyn-DIO-hM3D(Gq)-mCherry	Krashes et al., 2011		Addgene AAV5; 44361-AAV5
AAV5-EF1a-DIO-hChR2(H134R)-EYFP	Hope Center Viral Vectors Core		N/A
Cowpox virus Brighton Red	BEI Resources		NR-88
Zika-SMGC-1, GENBANK: KX266255	Isolated from patient (Wang et al., 2016)		N/A
Staphylococcus aureus	ATCC		ATCC 29213
Streptococcus pyogenes: M1 serotype strain: strain SF370; M1 GAS	ATCC		ATCC 700294
Biological Samples
Healthy adult BA9 brain tissue	University of Maryland Brain & Tissue Bank; http://medschool.umaryland.edu/btbank/		Cat#UMB1455
Human hippocampal brain blocks	New York Brain Bank		http://nybb.hs.columbia.edu/
Patient-derived xenografts (PDX)	Children’s Oncology Group Cell Culture and Xenograft Repository		http://cogcell.org/
Chemicals, Peptides, and Recombinant Proteins
MK-2206 AKT inhibitor	Selleck Chemicals		S1078; CAS: 1032350–13-2
SB-505124	Sigma-Aldrich		S4696; CAS: 694433–59-5 (free base)
Picrotoxin	Sigma-Aldrich		P1675; CAS: 124–87-8
Human TGF-β	R&D		240-B; GenPept: P01137
Activated S6K1	Millipore		Cat#14–486
GST-BMAL1	Novus		Cat#H00000406-P01
Critical Commercial Assays
EasyTag EXPRESS 35S Protein Labeling Kit	Perkin-Elmer		NEG772014MC
CaspaseGlo 3/7	Promega		G8090
TruSeq ChIP Sample Prep Kit	Illumina		IP-202–1012
Deposited Data
Raw and analyzed data	This paper		GEO: GSE63473
B-RAF RBD (apo) structure	This paper		PDB: 5J17
Human reference genome NCBI build 37, GRCh37	Genome Reference Consortium		http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Nanog STILT inference	This paper; Mendeley Data		http://dx.doi.org/10.17632/wx6s4mj7s8.2
Affinity-based mass spectrometry performed with 57 genes	This paper; and Mendeley Data		Table S8; http://dx.doi.org/10.17632/5hvpvspw82.1
Experimental Models: Cell Lines
Hamster: CHO cells	ATCC		CRL-11268
D. melanogaster: Cell line S2: S2-DRSC	Laboratory of Norbert Perrimon		FlyBase: FBtc0000181
Human: Passage 40 H9 ES cells	MSKCC stem cell core facility		N/A
Human: HUES 8 hESC line (NIH approval number NIHhESC-09–0021)	HSCI iPS Core		hES Cell Line: HUES-8
Experimental Models: Organisms/Strains
C. elegans: Strain BC4011: srl-1(s2500) II; dpy-18(e364) III; unc-46(e177)rol-3(s1040) V.	Caenorhabditis Genetics Center		WB Strain: BC4011; WormBase: WBVar00241916
D. melanogaster: RNAi of Sxl: y[1] sc[*] v[1]; P{TRiP.HMS00609}attP2	Bloomington Drosophila Stock Center		BDSC:34393; FlyBase: FBtp0064874
S. cerevisiae: Strain background: W303	ATCC		ATTC: 208353
Mouse: R6/2: B6CBA-Tg(HDexon1)62Gpb/3J	The Jackson Laboratory		JAX: 006494
Mouse: OXTRfl/fl: B6.129(SJL)-Oxtrtm1.1Wsy/J	The Jackson Laboratory		RRID: IMSR_JAX:008471
Zebrafish: Tg(Shha:GFP)t10: t10Tg	Neumann and Nuesslein-Volhard, 2000		ZFIN: ZDB-GENO-060207–1
Arabidopsis: 35S::PIF4-YFP, BZR1-CFP	Wang et al., 2012		N/A
Arabidopsis: JYB1021.2: pS24(AT5G58010)::cS24:GFP(-G):NOS #1	NASC		NASC ID: N70450
Oligonucleotides
siRNA targeting sequence: PIP5K I alpha #1: ACACAGUACUCAGUUGAUA	This paper		N/A
Primers for XX, see Table SX	This paper		N/A
Primer: GFP/YFP/CFP Forward: GCACGACTTCTTCAAGTCCGCCATGCC	This paper		N/A
Morpholino: MO-pax2a GGTCTGCTTTGCAGTGAATATCCAT	Gene Tools		ZFIN: ZDB-MRPHLNO-061106-5
ACTB (hs01060665_g1)	Life Technologies		Cat#4331182
RNA sequence: hnRNPA1_ligand: UAGGGACUUAGGGUUCUCUCUAGGGACUUAGGGUUCUCUCUAGGGA	This paper		N/A
Recombinant DNA
pLVX-Tight-Puro (TetOn)	Clonetech		Cat#632162
Plasmid: GFP-Nito	This paper		N/A
cDNA GH111110	Drosophila Genomics Resource Center		DGRC:5666; FlyBase:FBcl0130415
AAV2/1-hsyn-GCaMP6- WPRE	Chen et al., 2013		N/A
Mouse raptor: pLKO mouse shRNA 1 raptor	Thoreen et al., 2009		Addgene Plasmid #21339
Software and Algorithms
ImageJ	Schneider et al., 2012		https://imagej.nih.gov/ij/
Bowtie2	Langmead and Salzberg, 2012		http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools	Li et al., 2009		http://samtools.sourceforge.net/
Weighted Maximal Information Component Analysis v0.9	Rau et al., 2013		https://github.com/ChristophRau/wMICA
ICS algorithm	This paper; Mendeley Data		http://dx.doi.org/10.17632/5hvpvspw82.1
Other
Sequence data, analyses, and resources related to the ultra-deep sequencing of the AML31 tumor, relapse, and matched normal.	This paper		http://aml31.genome.wustl.edu
Resource website for the AML31 publication	This paper		https://github.com/chrisamiller/aml31SuppSite