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. 2023 Aug 23;3(9):100389. doi: 10.1016/j.xgen.2023.100389
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit monoclonal anti-MSH2 (D24B5) Cell Signaling Technology Cat.#2017S; RRID:AB_2235387
Mouse monoclonal anti-α-Tubulin (B-5-1-2) Sigma-Aldrich SKU T5168-100UL; RRID:AB_477579
Goat polyclonal anti-rabbit IgG IRDye 800CW Li-Cor P/N 926–32211; RRID:AB_621843
Goat polyclonal anti-mouse IgG IRDye 680RD Li-Cor P/N 926–68070; RRID:AB_10956588
Anti-human CD34-BV421 (clone 561) BioLegend Cat.#343610; RRID:AB_2561358
Anti-human Lineage Cocktail (CD3/CD14/CD19/CD20/CD56)-FITC (clones UCHT1, HCD14, HIB19, 2H7, HCD56) BioLegend Cat.#348801; RRID:AB_10612570
Anti-human CD38-PE (clone HIT2) BioLegend Cat.#303506; RRID:AB_314358
Anti-human CD90-APC (clone 5E10) BioLegend Cat.#328114; RRID: AB_893431
Anti-human CD45RA-PerCP/Cy5.5 (clone HI100) BioLegend Cat.#304122; RRID: AB_893357
Chemicals, peptides, and recombinant proteins
Mitomycin C from Streptomyces caespitosus Sigma-Aldrich SKU M4287-2MG
Critical commercial assays
ResolveDNA Whole Genome Amplification Kit BioSkryb 100545
QIAamp DNA Micro Kit QIAGEN Cat.#56304
DNeasy Blood & Tissue Kit QIAGEN Cat.#69506
Deposited data
Raw whole genome sequencing data This paper EGA: EGAS00001007288
Processed somatic variant data and western blots This paper Mendeley Data: https://doi.org/10.17632/c3r9chw9rb.1
Single-cell PTA-based WGS data from cord blood tissue Gonzalez-Pena et al.17 SRA: SRP178894
Experimental models: Cell lines
Human: AHH-1 ATCC CRL-8146; RRID:CVCL_3640
Oligonucleotides
Guide RNA FANCC: 5′-GCAAGAGATGGAGAAGTGTA-3′ This paper N/A
Guide RNA MSH2: 5′-GTGCCTTTCAACAACCGGTTG-3′ This paper N/A
Recombinant DNA
Plasmid: pSpCas9(BB)-2A-GFP (PX458) Ran et al.42 Addgene: #48138
Software and algorithms
PTATO This paper https://github.com/ToolsVanBox/PTATO;
https://doi.org/10.5281/zenodo.8098608
SMuRF v3.0.1 This paper https://github.com/ToolsVanBox/SMuRF
IAP v2.8.0 University Medical Center Utrecht https://github.com/UMCUGenetics/IAP
GRIDSS-PURPLE-LINX pipeline v1.3.2 Hartwig Medical Foundation https://github.com/hartwigmedical/gridss-purple-linx
SCAN2 Luquette et al.18 https://github.com/parklab/SCAN2
BWA v0.7.17 Li et al.43 https://github.com/lh3/bwa
GATK v4.1.3.0 DePristo et al.44 https://gatk.broadinstitute.org/hc/en-us
Picard v2.24.1 http://broadinstitute.github.io/picard
Samtools v1.9.4 Danecek et al.45 https://www.htslib.org/
Sambamba v0.8.2 Tarasov et al.46 https://github.com/biod/sambamba
Bedtools v.2.30.0 Quinlan and Hall47 https://bedtools.readthedocs.io/en/latest/
Nextflow v21.10.6.5661 Di Tommaso et al.48 https://www.nextflow.io/
GRIDSS2 v2.13.2 Cameron et al.34 https://github.com/PapenfussLab/gridss
GRIPSS Priestley et al.35 https://github.com/hartwigmedical/hmftools/tree/master/gripss
COBALT v1.11 Priestley et al.35 https://github.com/hartwigmedical/hmftools/tree/master/cobalt
ShapeIt v4.2.2 Delaneau et al.49 https://odelaneau.github.io/shapeit4/
Circos v0.69-9 Krzywinski et al.50 http://circos.ca/
MongoDB https://www.mongodb.com/
ggplot2 v3.4.1 Wickham51 https://ggplot2.tidyverse.org/
ggpubr v0.6.0 https://CRAN.R-project.org/package=ggpubr
rstatix v0.7.2 https://CRAN.R-project.org/package=rstatix
MutationalPatterns v3.6.0 Manders et al.52 https://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html
VariantAnnotation v1.42.1 Obenchain et al.53 https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html
StructuralVariantAnnotation v1.12 Cameron and Dong 202334 https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.html
BSgenome.Hsapiens.UCSC.hg38 v1.4.4 Pagès2023 https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html
randomForest v4.7–1.1 https://cran.r-project.org/package=randomForest
Copynumber v1.36 Nilsen, Liestoel and Lingjaerde https://bioconductor.org/packages/release/bioc/html/copynumber.html
LaplacesDemon v16.1.6 https://CRAN.R-project.org/package=LaplacesDemon
Seqkit v2.2.0 Shen et al.54 https://bioinf.shenwei.me/seqkit/
ggeffects v1.1.0 Lüdecke55 https://strengejacke.github.io/ggeffects/
TIDE Brinkman et al.56 https://tide.nki.nl/
IGV Robinson et al.57 https://software.broadinstitute.org/software/igv/
Other
Custom code to create figures This paper https://github.com/ProjectsVanBox/PTATO; https://doi.org/10.5281/zenodo.8186323