| Antibodies |
|
|
| Rat monoclonal anti-GFP |
Nacalai Tesque |
Cat#04404-84; RRID: AB_10013361 |
| Chicken polyclonal anti-GFAP |
Abcam |
Cat#ab4674; RRID: AB_304558 |
| Chicken polyclonal anti-TH |
Millipore |
Cat#ab9702; RRID: AB_570923 |
| Goat polyclonal anti-DCX |
Santa Cruz Biotechnology |
Cat#sc-8066; RRID: AB_2088494 |
| Rabbit polyclonal anti-CALB2 |
Millipore Sigma |
Cat#ab5054; RRID: AB_2068506 |
| Rabbit polyclonal anti-EOMES |
Millipore Sigma |
Cat#ab2283; RRID: AB_10806889 |
| Mouse monoclonal anti-PVALB |
Millipore Sigma |
Cat#mab1572; RRID: AB_2174013 |
| Rabbit polyclonal anti-DOT1L |
Abcam |
Cat#ab64077; RRID: AB_2095412 |
| Mouse monoclonal anti-RELN |
Millipore Sigma |
Cat#mab5364; RRID: AB_2179313 |
| Rabbit polyclonal anti-NOTUM |
Sigma |
Cat#abs762 |
| Rat monoclonal anti- mouse CD14 PECy7 |
BioLegend |
Cat#1223315; RRID: AB_10641133 |
| Mouse seroblock FcR |
BioRad |
Cat#Buf041A |
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| Papain |
Worthington |
Cat#LS003119
|
| PIPES |
Sigma |
Cat#P1851 |
| Ovomucoid |
Worthington |
Cat#LS003087
|
| Percoll |
Sigma |
Cat#P1644 |
| Calcein AM |
Invitrogen |
Cat#C3100MP |
| 2-Mercaptoethanol |
Fisher Scientific |
Cat#BP176-100 |
| Mouse recombinant EGF |
Thermofisher |
Cat# PMG8041 |
| Alexa Fluor 647 EGF |
Thermofisher |
E35351 |
| Recombinant Mouse Notum Protein |
R&D Systems |
Cat # 9150-NO-050 |
| N2 supplement |
Life Sciences |
17502048 |
| B27 supplement |
Life Sciences |
12587-010 |
| ABC99 |
Suciu et al., 2018 |
The Cravatt Lab |
| ABC101 |
Suciu et al., 2018 |
The Cravatt Lab |
| Critical Commercial Assays |
|
|
| Nextera XT DNA Library Preparation Kit |
Illumina |
Cat#FC-131-1024 |
| Qubit dsDNA HS Assay Kit |
ThermoFisher |
Cat#Q32854
|
| High Sensitivity DNA chips kit |
Agilent Technologies |
Cat#5067-4626 |
| NextSeq 500/550 High Output v2 kit (75 cycles) |
Illumina |
Cat#FC-404-2005 |
| SOLAμ™ SPE Plates |
Thermofisher |
Cat#60209-001 |
| EASY-Spray column |
Thermofisher |
Part# ES800 |
| DC™ Protein Assay Kit II |
BioRad |
Cat#5000112 |
| Millicell Cell Culture Insert |
Millipore Sigma |
Cat# PICM0RG50 |
| Deposited Data |
|
|
| Raw and processed data |
This manuscript |
GEO: GSE134918
|
| Experimental Models: Organisms/Strains |
|
|
| Mouse: C57BL/6J |
The Jackson Laboratory |
JAX: 00664 |
| Mouse: B6.Cg-Tg(GFAP-cre/ERT2)505Fmv/J |
The Jackson Laboratory |
JAX: 012849 |
| Mouse: B6;129S6-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze
|
The Jackson Laboratory |
JAX: 007908 |
| Mouse: ratNes::FLPOER
|
The Joyner lab |
Wojcinski et al., 2017 |
| Mouse: Rosa26FRT-STOP-FRT-TdTomato
|
The Jackson Laboratory |
JAX: 021875 |
| Mouse: Nestin-CFP
|
The Joyner lab |
Wojcinski et al., 2017 |
| Oligonucleotides |
|
|
| Template Switching Oligonucleotide AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG |
Macosko et al., 2015 |
IDT |
|
Gapdh primer F 5′- CCAAGGTGTCCGTCGTGGATCT-3′ |
https://pga.mgh.harvard.edu/primerbank/ |
IDT |
|
Gapdh primer R 5′- GTTGAAGTCGCAGGAGACAACC-3′ |
https://pga.mgh.harvard.edu/primerbank/ |
IDT |
|
Axin2 primer F 5′-TGACTCTCCTTCCAGATCCCA-3′ |
https://pga.mgh.harvard.edu/primerbank/ |
IDT |
|
Axin2 primer R 5′-TGCCCACACTAGGCTGACA-3′ |
https://pga.mgh.harvard.edu/primerbank/ |
IDT |
| Software and Algorithms |
|
|
| Phenograph |
Levine et al., 2015 |
https://github.com/jacoblevine/PhenoGraph |
| Force-directed graphs |
Weinreb et al., 2018 |
https://github.com/AllonKleinLab/SPRING/ |
| t- distributed stochastic neighbor embedding (t-SNE) |
Van der Maaten and Hinton, 2008 |
https://lvdmaaten.github.io/tsne/ |
| Rstudio |
R Studio Team (2015) |
https://www.rstudio.com |
| Gene Set Enrichment Analysis |
Subramanian et al., 2005 |
https://www.gsea-msigdb.org/gsea/index.jsp |
| SCDE |
Kharchenko et al., 2014 |
http://hms-dbmi.github.io/scde/ |
| scHPF |
Levitin et al., 2019 |
https://github.com/simslab/scHPF |
| Skyline |
|
https://skyline.ms/project/home/begin.view?/ |
| Other |
|
|
| DNase I |
Worthington |
Cat#LS002139
|
| Drop-seq beads |
ChemGenes |
Cat# MACOSKO-2011-10 |
| SCOPE-seq beads |
ChemGenes |
Custom Beads |
| Maxima H Minus Reverse Transcriptase |
ThermoFisher |
Cat#EP0752 |
| Exo-I |
New England Biolabs |
Cat#M0293L |
| SUPERaseIN |
ThermoFisher |
Cat#AM2696 |
| KAPA HotStart ReadyMix |
Kapabiosystems |
Cat#KK2602 |
| Ampure XP beads |
Beckman Coulter |
Cat#A63881 |
| Buffer TCL |
QIAGEN |
Cat#1031576 |
| miRNeasy RNA isolation kit |
QIAGEN |
Cat#217004 |
| iScript cDNA preparation kit |
BioRad |
Cat#1708890 |
