Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| AAVS1-Neo-M2rtTA | DeKelver et al.50 | Addgene Cat#60843 |
| Chemicals, peptides, and recombinant proteins | ||
| Accutase™ | STEMCELL Technologies |
Cat#07920 |
| Antibiotic-Antimycotic (100X) | ThermoFisher | Cat#15240062 |
| Blasticidin S hydrochloride | MilliporeSigma | Cat#15205 |
| (−)-Blebbistatin | MilliporeSigma | Cat#B0560 |
| CloneR | STEMCELL Technologies |
Cat#05888 |
| Doxycycline hyclate | MilliporeSigma | Cat#D9891 |
| DreamTaq Hot Start PCR Master Mix | ThermoFisher | Cat#K9012 |
| Geneticin™ Selective Antibiotic (G418 Sulfate) | ThermoFisher | Cat#10131035 |
| KAPA HiFi HotStart ReadyMix | Roche | Cat#07958935001 |
| KAPA SYBR FAST qPCR Kits | Roche | Cat#07959389001 |
| Lipofectamine™ Stem Transfection Reagent | ThermoFisher | Cat#STEM00001 |
| Matrigel Growth Factor Reduced Basement Membrane Matrix | Corning | Cat#354230 |
| mTeSR™ Plus | STEMCELL Technologies |
Cat#100–0276 |
| Opti-MEM I Reduced Serum Media | ThermoFisher | Cat#31985062 |
| Pifithrin-α hydrobromide | Tocris Bioscience | Cat#1267 |
| Puromycin dihydrochloride | MilliporeSigma | Cat#P8833 |
| QuickExtract™ DNA Extraction Solution | Lucigen | Cat#QE09050 |
| SYBR Green I Nucleic Acid Gel Stain | ThermoFisher | Cat#S7563 |
| Critical commercial assays | ||
| DNA Clean & Concentrator-5 | Zymo Research | Cat#D4014 |
| MiSeq Reagent Micro Kit v2 (300-cycles) | Illumina | Cat#MS-103–1002 |
| MycoAlert® PLUS Mycoplasma Detection Kit | Lonza | Cat#LT07–701 |
| Qubit dsDNA HS Assay Kit | ThermoFisher | Cat#Q32851 |
| Deposited data | ||
| Single-cell hgRNA sequencing raw FASTQ files for E1 and E2 | This study | SRP386685 |
| MARC1 sequencing data for determining hgRNA mutation rates | Kalhor et al.5
Leeper et al.30 |
SRP155997 |
| All quantitative fate maps | This study | 10.5281/zenodo.7112097 |
| inDelphi predicted mutant allele probabilities for hgRNAs in MARC1 mice and iPSC line | This study | 10.5281/zenodo.7112097 |
| Simulated phylogenies, sets of MARC1 hgRNAs used, single cell lineage barcodes, Phylotime reconstructed phylogenies for all experiments | This study | 10.5281/zenodo.7112097 |
| Experimental models: Cell lines | ||
| iPSC line: EP1-Cas9-hgRNA | This study | N/A |
| Oligonucleotides | ||
| See Table S3 for oligonucleotides used in this study. | This study | N/A |
| Recombinant DNA | ||
| Modified pSpCas9(BB)-2A-Puro (PX459) V2.0 | Eldred et al.45 | N/A |
| Modified Puro-Cas9 donor | Eldred et al.45 | N/A |
| PB-U6insert hgRNA library | Kalhor et al.5 | Addgene Cat#104536 |
| PB-U6insert-EF1puro library | Kalhor et al.5 | Addgene Cat#104537 |
| Super piggyBac Transposase expression vector | System Biosciences | Cat#PB210PA-1 |
| Software and algorithms | ||
| Cassiopeia | Jones et al.35 | https://github.com/YosefLab/Cassiopeia |
| ICE-FASE | This study |
https://github.com/Kalhor-Lab/QFM/ DOI: 10.5281/zenodo.7114804 |
| ImageJ | Schneider et al.51 | https://github.com/imagej/ImageJ |
| InDelphi | Shen et al.31 | https://github.com/rnaxwshen/inDelphi-model |
| Phylotime | This study |
https://github.com/Kalhor-Lab/QFM/ DOI: 10.5281/zenodo.7114804 |
| MARC1 analysis pipeline | Leeper et al.30 | https://github.com/Kalhor-Lab/MARC1-Pipeline |
| Other | ||