Key resources table.
| Reagent type | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | PCNA (mouse monoclonal) | BioLegend | cat# 307901, RRID:AB_314691 | 1:300 |
| Antibody | BrdU (rat monoclonal) | Abcam | cat# ab6326, RRID:AB_314691 | 1:200 |
| Antibody | SOX2 (rabbit polyclonal) | Abcam | cat# ab97959, RRID:AB_2341193 | 1:200 |
| Antibody | DIG conjugated to alkaline phosphatase (sheep polyclonal) | Sigma-Aldrich | cat# 11093274910, RRID:AB_2734716 | 1:2000 |
| Antibody | Alexa Fluor-488 (goat anti-rat IgG) | Thermo Fisher Scientific | cat# A-11006, RRID:AB_2534074 | 1:400 |
| Antibody | Alexa Fluor-568 (goat anti-rabbit IgG) | Thermo Fisher Scientific | cat# A-11011, RRID:AB_143157 | 1:400 (with SOX2), 1:600 (with PCNA) |
| Sequence-based reagent | PITX2 | This paper | PCR primers | Forward primer (fp) ATGAACTGCCTGAAAGACGC; reverse primer (rp) CATCAGGCCGTTGAATTGGG |
| Sequence-based reagent | LEF1 | This paper | PCR primers | (fp) GCCACCGACGAGATGATCC; (rp) GTGCGAAGGATGTGTCCCTG |
| Sequence-based reagent | SHH | Di-Poï and Milinkovitch (2016) | PCR primers | (fp) CAAGCAGTTCCATCCCCAAC; (rp) GCCCAGCTATGCTCCTCAAT |
| Sequence-based reagent | NOTCH1 | This paper | PCR primers | (fp) GCCACATC CTGGACTACGAC; (rp) GGAATGTCCAGGTTCCCGAG |
| Sequence-based reagent | LGR5 | This paper | PCR primers | (fp) GGAATGTCCAGGTTCCCGAG; (rp) GGCACTAGTGAATTGCTGGGG |
| Sequence-based reagent | IGFBP5 | This paper | PCR primers | (fp) GCAGAGGAGACCTTCCAACC; (rp) CTGAGGGCTTCTCACACCAG |
| Sequence-based reagent | ALX1 | This paper | PCR primers | (fp) CTGTCTCCCGTGAAAGGC AT; (rp) TAACAG AAGTGGGTGACTGCC |
| Sequence-based reagent | SIX3 | This paper | PCR primers | (fp) TGCCCACG CTCAACTTTTC; (rp) CCGCCGAA CTGTGAGTAGGA |
| Sequence-based reagent | ISL1 | This paper | PCR primers | (fp) ACCTGCTTT GTTAGGGACGG; (rp) CGTCGTG TCTCTCCGGAC TA |
| Sequence-based reagent | ALX1 | This paper | qPCR primers | (fp) GCAGTTCC GTTGTGACTTC; (rp) ATCTGTCC GAGGTGAATGG |
| Sequence-based reagent | SIX3 | This paper | qPCR primers | (fp) CTCTACCAC ATCCTGGAGAAC; (rp) TTCCTGG TAGTGAGCTTCG |
| Sequence-based reagent | ISL1 | This paper | qPCR primers | (fp) TGCGGCA ATCAAATCCAC; (rp) GGTTACATT CCGCACACTTC |
| Sequence-based reagent | FOXI1 | This paper | qPCR primers | (fp) GGCTATAC TGGTTCAGTCCTC; (rp) ACTTCA GTGCCCTCTCTTG |
| Sequence-based reagent | BARX1 | This paper | qPCR primers | (fp) AAGGTGGA GGGCTTGAATC; (rp) TGTCAACT GCTCGCTACTG |
| Sequence-based reagent | ACTB | This paper | qPCR primers | (fp) CCTGGAGA AGAGCTACGAAC; (rp) AGAAAG ACGGCTGGAAGAG |
| Commercial assay or kit | RNeasy Plus Micro Kit | Qiagen | cat#/ID: 74034 | |
| Commercial assay or kit | Ovation SoLo RNA-Seq Library Preparation Kit | Nugen | cat#/ID: 0501–32 |
|
| Commercial assay or kit | RNA 6000 Pico Kit | Agilent | cat#: 5067–1513 |
|
| Commercial assay or kit | QuantiTect Reverse Transcription Kit | Qiagen | cat#/ID: 205311 | |
| Commercial assay or kit | iTaq Universal SYBR Green Supermix | Bio-Rad | cat#: 1725121 |
|
| Commercial assay or kit | TUNEL in situ cell death detection | Roche | cat#: 11684795910 | |
| Chemical compound, drug | BrdU | Sigma-Aldrich | cat#: B5002 | Administered at 80 mg/kg |
| Chemical compound, drug | DiI | Biotium | cat#: 60010 | Dissolved into ethanol at 25 mg/ml; working solution further diluted in 0.3M sucrose at 5 mg/ml |
| Chemical compound, drug | Fluoroshield mounting medium | Sigma-Aldrich | cat#: F6057 |
|
| Chemical compound, drug | Dako Faramount aqueous medium | Agilent | cat#: S302580 |
|
| Software, algorithm | Nrecon | Bruker | ||
| Software, algorithm | Advanced 3D Visualization and Volume Modeling (Amira) | Thermo Fisher Scientific | RRID:SCR_007353 | |
| Software, algorithm | Fiji/ImageJ | Schindelin et al. (2012) | RRID:SCR_002285 | |
| Software, algorithm | Adobe Photoshop CC | Adobe | RRID:SCR_014199 | |
| Software, algorithm | NIS-Elements | Nikon | RRID:SCR_014329 | |
| Software, algorithm | Leica Application Suite X | Leica | RRID:SCR_013673 | |
| Software, algorithm | Microsoft Excel | Microsoft | RRID:SCR_016137 | |
| Software, algorithm | Zen | Zeiss | RRID:SCR_013672 | |
| Software, algorithm | FastQC | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | RRID:SCR_014583 | |
| Software, algorithm | Trimmomatic | Bolger et al. (2014) | RRID:SCR_011848 | |
| Software, algorithm | SortMeRNA | Kopylova et al. (2012) | RRID:SCR_014402 | |
| Software, algorithm | STAR | Dobin et al. (2013) | RRID:SCR_015899 | |
| Software, algorithm | edgeR | Robinson et al. (2010) | RRID:SCR_012802 | |
| Software, algorithm | PALM Robo | Zeiss | RRID:SCR_014435 | |
| Software, algorithm | CFX Manager | Bio-Rad | RRID:SCR_017251 | |
| Other | PALM MicroBeam device | Zeiss |