KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
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| Antibodies | ||
|
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| Mouse anti-Flag | Sigma-Aldrich | Cat# F1804; RRID: AB_262044 |
| Goat anti-Mcm2 | R&D Systems | Cat# AF5778; RRID: AB_2141963 |
| Rabbit anti-Geminin | Proteintech | Cat# 10802–1-AP; RRID: AB_2110945 |
| Rabbit anti-phospho-histone H3 (SER10) | Cell Signaling Technology | Cat# 53348S; RRID: AB_2799431 |
| Rabbit anti-Sox9 | Millipore | Cat# AB5535; RRID: AB_2239761 |
| Rabbit anti-Nfix | Thermo Fisher Scientific | Cat# PA5–30897; RRID: AB_2548371 |
| Goat anti-GFP | Rockland Inc. | Cat#600–101-215 RRID: AB_218182 |
| Mouse anti-Mcm2 (BM28) | BD Biosciences | Cat#610701 RRID: AB_398024 |
| Rabbit anti-Hopx | Proteintech | Cat# 11419–1-AP; RRID: AB_10693525 |
| Rabbit anti-Prox1 | Abcam | Cat# ab199359; RRID: AB_2868427 |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| DAPI | Roche | 10236276001 |
| DAPI | BD Biosciences | 564907 |
| Paraformaldehyde | Electron Microscopy Sciences | 100504–162 |
| Triton X-100 | Sigma-Aldrich | T9284 |
| Donkey serum | Millipore-Sigma | S30–100ML |
| TFM Tissue Freezing Medium | GeneralData | TFM-5 |
| ProLong™ Gold Antifade Mountant | Thermo Fisher Scientific | P36930 |
| Percoll | GE Healthcare | 17–0891-02 |
| Hibernate A | Brain Bits | HA |
| Hibernate A Low Fluorescence | Brain Bits | HALF |
| Hibernate E Low Fluorescence | Brain Bits | HELF |
| MitoTracker™ Deep Red FM - Special Packaging | Thermo Fisher Scientific | M22426 |
| Dihydroethidium | Thermo Fisher Scientific | D1168 |
| Autophagy Assay Kit (Red) | Abcam | ab270790 |
| Target Retrieval Solution, Concentrated x 10 | Agilent Dako | S169984–2 |
| Chloroquine diphosphate salt | Sigma-Aldrich | C6628–25G |
| Bafilomycin A1 | Sigma-Aldrich | 19–148 |
| OPP (O-propargyl-puromycin) | Click Chemistry Tools | 1407–5 |
| DMEM | Gibco | 11965084 |
| Fetal Bovine Serum | Hyclone | SH30071.03 |
| Glutamax | Gibco | 35050061 |
| Penicillin-Streptomycin | Gibco | 15140122 |
| Poly-L-lysine | Sigma-Aldrich | P2636 |
| B-27 | Gibco | 17504044 |
|
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| Critical commercial assays | ||
|
| ||
| MACS Neural Tissue Dissociation Kit (P) | Miltenyi Biotec | 130–092-628 |
| Click-iT™ Plus OPP Alexa Fluor™ 647 Protein Synthesis Assay Kit | Thermo Fisher Scientific | C10458 |
| Agencourt RNAClean XP | Beckman Coulter | A63987 |
| SMARTScribe Reverse Transcriptase | Clontech | 639538 |
| Advantage 2 PCR Kit | Clontech | 639206 |
| KAPA HiFi PCR Kit with dNTPs | KAPA | KK2102 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher Scientific | Q32854 |
| EZ-Tn5 Custom Transposome Construction Kit with pMOD-2 Transposon Construction Vector | Epicenter | TNP10622 |
| 75-cycle High Output Kit v2.5 | Illumina | 20024906 |
| Click-iT™ Plus EdU Alexa Fluor™ 647 Flow Cytometry Assay Kit | Thermo Fisher Scientific | C10634 |
|
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| Deposited data | ||
|
| ||
| scRNA-seq data | This Paper | NCBI GEO: GSE232833 |
|
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| Experimental models: Organisms/strains | ||
|
| ||
| Mouse: Hopxtm3.1Joe/J | The Jackson Laboratory | Cat# 029271; RRID: IMSR_JAX:029271 |
| Mouse: GFP-LC3 | RIKEN BioResource Research Center |
Cat# RBRC00806; RRID: IMSR_RBRC00806 |
| Mouse: C57BL/6NCrl | Charles River Laboratory | Cat# CRL:27; RRID: IMSR_CRL:27 |
| Mouse: Hopxtm2.1(cre/ERT2)Joe/J | The Jackson Laboratory | Cat# 017606; RRID: IMSR_JAX:017606 |
| Mouse: B6.129(Cg)-Gt(ROSA) 26Sortm4(ACTB-tdTomato,EGFP)Luo/J |
The Jackson Laboratory | Cat# 007676; RRID: IMSR_JAX:007676 |
| Mouse: B6.129S-Atg5<tm1Myok> | RIKEN BioResource Research Center | Cat# RBRC02975; RRID: IMSR_RBRC02975 |
|
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| Oligonucleotides | ||
|
| ||
| SMARTSeq_CDS_Primer | AACGAGTGGAATCACTG CTGAGTACTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTVN |
|
| SMARTSeq_Amp | AACGAGTGGAATCACTGCTGAGT | |
| SMARTSeq_TSO_RNAOligo | AACGAGTGGAATCACTGCTG AGTACATrGrG+G |
|
|
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| Software and algorithms | ||
|
| ||
| Code | This Paper | GitHub: https://github.com/dvjim/AtoQ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| GraphPad Prism | GraphPad Software Inc | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo | FlowJO, LLC | https://www.flowjo.com/ |
| BD FACSDiva™ | BD Biosciences | https://www.bdbiosciences.com/en-us/products/software/instrument-software/bd-facsdiva-software |
| R | Open source | https://www.r-project.org/ |
| RSEM | Li and Dewey135 | https://deweylab.github.io/RSEM/ |
| Cutadapt | Martin136 | https://cutadapt.readthedocs.io/en/stable/ |
| Samtools | Li et al., 2009137 | http://www.htslib.org/ |
| Monocle | Qiu et al.138 | http://cole-trapnell-lab.github.io/monocle-release/ |
| Clustree | Zappia and Oshlack139 | http://lazappi.github.io/clustree. |
| Seurat | Satija and Hafemeister, 2019140; Hao et al., 2020141 | https://satijalab.org/seurat/ |
| Tximport | Soneson et al.142 | https://github.com/mikelove/tximport |
| CellRouter | Lummertz da Rocha et al.57 | https://github.com/edroaldo/cellrouter |
| bluster | Lun and Hicks143 | https://bioconductor.org/packages/release/bioc/html/bluster.html |
| ClusterProfiler | Yu et al.144 | https://yulab-smu.top/software/ |
| VelocytoR | La Manno et al.46 | http://velocyto.org/ |
| STAR | Dobin et al.145 | https://github.com/alexdobin/STAR/releases |
| SCENIC | Aibar et al.146 | https://scenic.aertslab.org/ |
| Adobe Illustrator | Adobe | https://www.adobe.com/products/illustrator.html; RRID: SCR_010279 |
| Adobe Photoshop | Adobe | https://www.adobe.com/products/photoshop.html; RRID:SCR_014199 |
| Zen 2 | Carl Zeiss | https://www.zeiss.com; RRID: SCR_013672 |
| scuttle | Lun et al.147; McCarthy et al.148 | https://bioconductor.org/packages/release/bioc/html/scuttle.html |
|
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| Other | ||
|
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| Fluorodish | World Precision Instruments | FD35–100 |