Key Resource Table
| REAGENT OR RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Antibodies | |||
| b-actin | Abcam | Cat #ab8227; RRID: AB_2305186 | |
| ADAR1 | Abcam | Cat #ab126745; RRID: AB_11145661 |
|
| APOBEC3C | Abcam | Cat # ab72652; RRID: AB_ 1523141 |
|
| pSTAT3 (Y705)-FITC | eBioscience | Cat # 11–9033-42; RRID: AB_2572522 |
|
| CD34 BV421 | BD | Cat # 740081; RRID: AB_2739844 |
|
| ADAR1 | Abcam | Cat # 126745; RRID: AB_ 11145661 |
|
| ADAR1 | Cell Signaling | Cat # 14175; RRID: AB_ 2722520 |
|
| STAT3 (124H6) | Cell Signaling | Cat # 9139; RRID: AB_ 331757 |
|
| p-STAT3 Y705 | Cell Signaling | Cat # 9131; RRID: AB_ 2331586 |
|
| GAPDH | Millipore | Cat # MAB374; RRID: AB_ 2107445 |
|
| CDK13 | Abcam | Cat # ab251955 | |
| ADAR1-APC | Abcam | Cat # ab168809 | |
| APOBEC3C | Abcam | Cat # ab221874; RRID: AB_ 2722520 |
|
| GAPDH | Abcam | Cat # ab181602; RRID: AB_2630358 |
|
| Goat pAb Rb IgG AF568 | Abcam | Cat # ab175471; RRID: AB_2576207 |
|
| Goat pAb Rb IgG AF568 | Abcam | Cat # ab150077; RRID: AB_2630356 |
|
| HRP-linked anti-rabbit IgG | Cell Signaling | Cat # 7074; RRID: AB_2099233 |
|
| HRP-linked anti-mouse IgG | Cell Signaling | Cat # 7076; RRID: AB_330924 |
|
| CD45-Alexa405 | Invitrogen | Cat #MHCD4526; RRID: AB_10372211 | |
| CD38-Alexa647 | Ab Serotec | Cat #MCA1019A647; RRID: AB_324854 | |
| CD34-Biotin | Invitrogen | Cat #CD3458115; RRID: AB_2536503 | |
| Strepavidin-Alexa488 | Invitrogen | Cat #S32354; RRID: AB_2315383 | |
| 7AAD | Invitrogen | Cat #A1310 | |
| Alexa Fluor® 594 Goat Anti- Rabbit IgG (H+L) Antibody |
Invitrogen | Cat #A11012; RRID: AB_10562717 |
|
| CD45-APC | Invitrogen | Cat #MHCD4505; RRID: AB_10372216 | |
| CD45-BB515 | BD | Cat #564585; RRID: AB_2732068 | |
| CD34-BV 421 | BD | Cat # 562577; RRID: AB_2687922 | |
| CD38-PE-Cy7 | BD | Cat #335790; RRID: AB_399969 | |
| CD123-PE | BD | Cat #554529; RRID: AB_395457 | |
| CD45RA-FITC | Invitrogen | Cat #MHCD45RA01; RRID: AB_10373858 | |
| CD8-PE-Cy 5.5 | BD | Cat #555368; RRID: AB_395771 | |
| CD56- PE-Cy 5.5 | BD | Cat #555517; RRID: AB_395907 | |
| CD4- PE-Cy 5.5 | BD | Cat #555348; RRID: AB_395753 | |
| CD3- PE-Cy 5.5 | BD | Cat #555334; RRID: AB_395741 | |
| CD19- PE-Cy 5.5 | BD | Cat #555414; RRID: AB_395814 | |
| CD2- PE-Cy 5.5 | BD | Cat #555328; RRID: AB_395735 | |
| CD14- PerCP-Cy5.5 | BD | Cat # 550787; RRID: AB_393884 | |
| CD8-PE-Cy 5.5 | BD | Cat #555368; RRID: AB_395771 | |
| CD56- PE-Cy 5.5 | BD | Cat #555517; RRID: AB_395907 | |
| CD3-FITC | BioLegend | Cat #300306; RRID: AB_314042 | |
| Bacterial and Virus Strains | |||
| DH5alpha Competent E. Coli | Invitrogen | Cat #12297016 | |
| Stbl2 Competent E. Coli | Invitrogen | Cat #10268019 | |
| Biological Samples | |||
| Aged normal and MPN Patient samples | Obtained through patients consenting at UCSD Moores Cancer Center according to Institutional Review Boardapproved protocols. | N/A | |
| Young Cord blood CD34+ cells | Purchased from AllCells or StemCell Technologies |
Cat #CB008F-S Cat #70008.5 Cat #70008.2 |
|
| Critical Commercial Assays | |||
| SYBR GreenER qPCR SuperMix |
Invitrogen | Cat #11761–500 | |
| SuperScript III First-Strand Synthesis SuperMix for qRT- PCR |
Invitrogen | Cat #11752–250 | |
| Prolong Gold antifade reagent with DAPI | Invitrogen | Cat # P36935 | |
| Live/Dead Fixable Near IR Dead Cell Stain kit |
Invitrogen | Cat #L10119 | |
| Secrete-Pair Dual Luminescence Assay Kit |
GeneCopoeia | Cat #LF033 | |
| Experimental Models: Cell Lines | |||
| K562 | ATCC | Cat #CCL-243; RRID: CVCL_0004 | |
| TF1a | ATCC | Cat #CRL-2451; RRID: CVCL_3608 | |
| 293T | ATCC | Cat #CRL-3216; RRID: CVCL_0063 | |
| Experimental Models: | |||
| Recombinant DNA | |||
| pCDH-EF1-MCS-T2A-copGFP | SBI System Biosciences | Cat #CD521A-1 | |
| pCDH-ADAR1 WT | Zipeto et al, 2016 | N/A | |
| pCDH-ADAR1E912A | Zipeto et al, 2016 | N/A | |
| pCDH-CMV-EF1-copGFP | SBI System Biosciences | Cat #CD511B-1 | |
| shADAR1-pLKO.1 (CCGGACCTCCTCACGAGCCCA AGTTCGTTTACCAAGCAAAA) |
This paper | N/A | |
| shScramble -pLKO.1 (CCTAAGGTTAAGTCGCCCTCG ) |
This paper | N/A | |
| Equipment | |||
| Olympus FluoView FV10i | Jamieson laboratory | N/A | |
| MACSQuoant 10 Analyzer | Jamieson laboratory | N/A | |
| Deposited Data | |||
| RNA-sequencing dataset | This paper | dbGAP: PHS002228.v1.p1. |
|
| DNA-sequencing dataset | This paper. | dbGAP: PHS002228.v1.p1. |
|
| Analysis codes | This paper | Github: https://github.com/ucsdccbb/MPN_atlas_methods | |
| Software and Algorithms | |||
| Burrows-Wheeler Aligner | Li H., 2013 | https://github.com/lh3/bwa | |
| VarScan2 | Koboldt et al., 2012 | https://dkoboldt.github.io/varscan/ | |
| Strelka2 | Kim et al., 2018 | https://github.com/Illumina/strelka | |
| MuSE | Fan et al. 2016 | https://bioinformatics.mdanderson.org/publicsoftware/muse/ | |
| Mutect2 | Benjamin et al., 2019 | https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2 | |
| SigProfilerMatrixGenerator | Bergstrom et al., 2019 | https://github.com/AlexandrovLab/SigProfilerMatrixGenerator | |
| Cutadapt v1.15 | Martin, 2011 | https://github.com/marcelm/cutadapt | |
| samblaster | Faust, et al., 2014 | https://github.com/GregoryFaust/samblaster | |
| Sambamba v0.4.7 | Tarasov, et al., 2015 | https://lomereiter.github.io/sambamba/ | |
| Samtools, v1.1 | Li et al., 2009 | http://www.htslib.org/ | |
| PicardTools v1.96 | https://broadinstitute.github.io/picard/ | ||
| Genome Analysis Tool Kit v2.4–9; v3.8 |
McKenna et al., 2010 | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit | |
| bwa-mem v0.7.12 | Li and Durbin, 2009 | http://biobwa.sourceforge.net/bwa.shtml)) | |
| STAR v2.5.1a; v2.5.2b | Dobin et al., 2013 | https://github.com/alexdobin/STAR | |
| RSEM v1.3.0 | Li & Dewey, 2011 | https://deweylab.github.io/RSEM/ | |
| ENCODE long RNA-seq Pipeline |
https://github.com/ENCODE-DCC/long-rna-seqpipeline | ||
| FastQC | Andrews, et al., 2012 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc// | |
| REDItools | Picardi & Pesole, 2013 | http://srv00.recas.ba.infn.it/reditools/ | |
| CrossMap | Zhao et a., 2014 | http://crossmap.sourceforge.net/ | |
| Mutect v1.1.5 | Cibulskis, et al., 2013 | https://software.broadinstitute.org/cancer/cga/mutect | |
| Bedtools v2.22.1; v2.26.0 | Quinlan & Hall, 2010 | http://bedtools.readthedocs.io/en/latest/ | |
| EdgeR | Robinson et al., 2010 | http://bioconductor.org/packages/release/bioc/html/edgeR.html | |
| Vcftools | Danecek, et al., 2011 | https://vcftools.github.io/index.html | |
| GENE-E | https://software.broadinstitute.org/GENE-E/ | ||
| Cirrus-ngs | https://github.com/ucsdccbb/cirrus-ngs | ||
| R v3.4.3 | https://cran.r-project.org/ | ||
| limma | Ritchie et al., 2015 | https://www.bioconductor.org/packages/release/bioc/html/limma.html | |
| limma-voom | Law et al., 2014 | https://www.bioconductor.org/packages/release/bioc/html/limma.html | |
| ANNOVAR v2017Jun01 | Wang, et al., 2010 | http://annovar.openbioinformatics.org/ | |
| SPIA | Tarca, et al., 2020 | https://bioconductor.org/packages/release/bioc/html/SPIA.html | |
| VariantAnnotation v1.24.5 | Obenchain, et al., 2014 | https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html | |
| SNPiR | https://github.com/rpiskol/SNPiR | ||
| Oncotator v1.9.8 | Ramos, et al., 2015 | https://software.broadinstitute.org/cancer/cga/oncotator | |
| bcl2fastq | https://support.illumina.com/sequencing/sequencing_software/bcl2fastqconversion-software.html | ||
| GProfiler | |||
| Cytoscape v3.7.1 | https://cytoscape.org/ | ||
| VisJS2Jupyter | Rosenthal, et al., 2018 | https://github.com/ucsdccbb/visJS2jupyter | |
| Rtsne, v0.15 | https://github.com/jkrijthe/Rtsne | ||
| Rcircos | Zhang, et al. 2013 | https://cran.r-project.org/web/packages/RCircos/index.html | |
| CNVkit | Talevich, et al. 2014 | https://cnvkit.readthedocs.io/en/stable/ | |
| Lumpy | Layer, et al. 2014 | https://github.com/arq5x/lumpy-sv | |
| Manta | Chen, et al., 2016 | https://github.com/Illumina/manta | |
| AnnotSV | Geoffrey, et al. 2018 | https://lbgi.fr/AnnotSV/ | |
| SURVIVOR | Jeffares, et al. 2017 | https://github.com/fritzsedlazeck/SURVIVOR | |
| Databases/Reference Datasets | |||
| 1000 Genomes Project | 1000G_phase1.snps.high _confidence.hg19.sites.vcf | ||
| dbSNP hg19 v138 | dbsnp_138.hg19.vcf | ||
| Hg19 fasta | ucsc.hg19.fasta | ||
| GRCh37v87 gtf | Homo_sapiens.GRCh37.8 7.gtf.gz |
||
| STRING high confidence interactome |
Szklarczyk et al., 2015 | 9606.protein.links.v11.0.txt | |
| ExAC | Lek, et al. 2016 | http://exac.broadinstitute.org/ | |
| gnomAD | https://gnomad.broadinstitute.org/ | ||
| DARNED | Kiran & Baranov, 2010 | rnaEditDB.txt | |
| RADAR v2 hg19 | Ramaswami & Li, 2014 | Human_AG_all_hg19_v2.t | |
| xt | |||
| GSVA | Hanzelmann et al, 2013 | https://bioconductor.org/packages/release/bioc/html/GSVA.html | |
| ICGC PCAWG MPN dataset | Campbell et al, 2020 | http://dcc.icgc.org/pcawg/ | |
| Other | |||
| Normal HSPC, CML CP progenitor, and BC CML progenitor gene expression |
Jiang et al, 2013 | BioProject: PRJNA214016 | |
| Cord blood CD34+ transduced with pCDH, ADAR1 WT, or ADAR1E912A |
Zipeto et al, 2016 | BioProject: PRJNA319866 | |