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. Author manuscript; available in PMC: 2022 Mar 13.
Published in final edited form as: Cell Rep. 2022 Jan 18;38(3):110251. doi: 10.1016/j.celrep.2021.110251

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit polyclonal antibody against GNMSELPPYQDTMR peptide from rat/chick Nkx2-1 Ohyama et al., 2005 N/A
Mouse monoclonal antibody against chicken Pax6 Developmental Studies Hybridoma Bank (DSHB) Cat# Pax6, RRID:AB_528427
Biological samples
Chicken Hypothalamus samples: dissected from fertilised Bovan Brown eggs Henry Stewart & Co., Norfolk, UK N/A
Chemicals, peptides, and recombinant proteins
Dispase I Roche Cat No. 4942086001
Hibernate-E media BrainBits LLC Cat No. HE500
Papain Worthington Chemicals Cat No. LS003119
B27 ThermoFisher Cat No. 17504044
GlutaMAX ThermoFisher Cat No. 35050061
RNase Inhibitor Promega Cat No. N2615
Recombinant Mouse Follistatin 288 (FS-288) R&D Systems Cat No. 769-FS-025
Human Follistatin Affinity Purified Polyclonal Ab R&D Systems Cat No. AF669
Critical commercial assays
Chromium Single Cell 3′ Library and Gel Bead Kit v3 10x Genomics Cat# 1000075
Chromium Single Cell 3′ Chip Kit B 10x Genomics Cat# 1000073
Chromium i7 Multiplex Kit 10x Genomics Cat# 120262
Deposited data
Chicken Raw and analyzed scRNA-Seq data This paper GSE171649
Mouse analyzed scRNA-Seq data (Kim et al., 2020) GSE132355
Human analyzed scRNA-Seq data (Zhou et al., 2020) GSE118487
Experimental models: organisms/strains
Chicken (Gallus gallus): Fertilised Bovan brown eggs Henry Stewart & Co., Norfolk, UK N/A
Oligonucleotides
Chicken ARX custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_025146483.1
Chicken BMP7 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_417496.6
Chicken CA2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205317.1
Chicken CHRD custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204980.2
Chicken DBX1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001199474.1
Chicken DLX1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. ENSGALT00000006647.6
Chicken ELAVL4 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204830.1
Chicken EMX2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_025152058.1/ XM_025152057.1
Chicken FGF10 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204696.1
Chicken FOXA1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_004941922.3
Chicken FOXA2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204770.1
Chicken FOXG1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205193.1
Chicken FST custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_015277250.2
Chicken HCRT custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204185.2
Chicken HOXB1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001080859.2
Chicken ISL1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205414.1
Chicken KRT20 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001277981.1
Chicken LHX9 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205426.1
Chicken MEIS2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_015287280.2
Chicken MSX1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205488.2
Chicken NEUROG1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204883.1
Chicken NHLH1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204121.1
Chicken NKX2-1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204616.1
Chicken NKX2-2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_015283379.2
Chicken NR5A1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205077.1
Chicken OLIG2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001031526.1, NC_006088.5|:106522977-106525323 #256 chromosome 1, GRCg6a
Chicken OTP custom designed probe set, HCR v3.0 Molecular Instruments, Inc. ENSGALT00000045360.3
Chicken PAX6 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205066.1
Chicken PITX2 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_205010.1/ XM_025149516.1/ XM_025149515.1
Chicken PROX1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001005616.1
Chicken RAX custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001243724.1
Chicken SHH custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204821.1
Chicken SIM1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. XM_004940357.3
Chicken SIX6 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204994.1
Chicken SP8 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_001198666.1
Chicken SST custom designed probe set, HCR v3.0 Molecular Instruments, Inc. ENSGALG00000007361
Chicken VAX1 custom designed probe set, HCR v3.0 Molecular Instruments, Inc. NM_204799.2/ XM_025151484.1
HCR v3.0 amplifier B1, Alexa Fluor-488 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B2, Alexa Fluor-488 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B3, Alexa Fluor-488 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B4, Alexa Fluor-488 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B5, Alexa Fluor-488 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B1, Alexa Fluor-546 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B2, Alexa Fluor-546 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B3, Alexa Fluor-546 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B4, Alexa Fluor-546 Molecular Instruments, Inc. N/A
HCR v3.0 amplifier B5, Alexa Fluor-546 Molecular Instruments, Inc. N/A
HCR Probe Hybridisation Buffer Molecular Instruments, Inc. N/A
HCR Probe Wash Buffer Molecular Instruments, Inc. N/A
HCR Amplification Buffer Molecular Instruments, Inc. N/A
Software and algorithms
Adobe Photoshop v22.3.0 Adobe Systems http://www.adobe.com
Adobe Illustrator v25.2.1 Adobe Systems http://www.adobe.com
CellRanger v.3.10 10x Genomics http://10xgenomics.com
R v3.6.1 The R project https://www.r-project.org
Seurat v3.1.5 (Butler et al., 2018) https://satijalab.org/seurat/
Harmony v1.0 (Korsunsky et al., 2019) https://github.com/immunogenomics/harmony
Scanpy v1.5.1 (Wolf et al., 2018) https://scanpy.readthedocs.io/en/stable/
scVelo v0.2.1 (Bergen et al., 2020) https://scvelo.readthedocs.io/
Monocle v3.0.2 (Trapnell et al., 2014) https://cole-trapnell-lab.github.io/monocle3/
NicheNet v0.1.0 (Browaeys et al., 2020) https://github.com/saeyslab/nichenetr
genesorteR v0.4.3 (Ibrahim and Kramann) https://github.com/mahmoudibrahim/genesorteR
Kallisto v0.46.2 (Melsted et al., 2021) https://www.kallistobus.tools/
Bustools v2.27.9 (Melsted et al., 2021) https://www.kallistobus.tools/
Homologene v1.4.68.19.3.27 https://github.com/oganm/homologene