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. 2023 Sep 14;3(10):100409. doi: 10.1016/j.xgen.2023.100409
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Recombinant rabbit monoclonal anti-fibroblast activation protein alpha (FAP) IgG, clone EPR20021 Abcam Cat# ab207178; RRID:AB_2864720
Rat monoclonal anti-MRC1 IgG2a, clone MR5D3 Thermo Fisher Scientific Cat# MA5-16868; RRID:AB_2538346
Polyclonal goat anti-rabbit IgG Alexa Fluor 647 Molecular Probes Cat# A-21245; RRID:AB_141775
Polyclonal goat anti-rat IgG Cy3 Abcam Cat# ab6953; RRID:AB_955010
Mouse monoclonal anti-pan cytokeratin IgG1 AF488, clone AE1/AE3 Thermo Fisher Scientific Cat# 53-9003-82; RRID:AB_1834350
Biological samples
Human FFPE thyroid samples Vanderbilt University Medical Center (VUMC) and the University of Washington Medical Center (UWMC) N/A
Critical commercial assays
truXTRAC FFPE Total NA Kit COVARIS 520220
Ultra II DNA Library Prep kit NEB E7645L
Visium Spatial Gene Expression Slide Kit 10x Genomics PN-1000188
Deposited data
ExAC (Exome Aggregation Consortium) Lek et al.49 http://exac.broadinstitute.org/
1000G (1000 Genomes Project) Lek et al.49 https://www.internationalgenome.org/
gnomAD (Genome Aggregation Database) Karczewski et al.50 https://gnomad.broadinstitute.org/
GENCODE GRCh38.p13 genome Frankish et al.51 https://www.gencodegenes.org/human/release_38.html
Gene Ontology Consortium resource Ashburner et al.,52 Aleksander et al.53 http://geneontology.org/
cBioPortal (TCGA Thyroid Carcinoma) Network CGAR,14Gao et al.,54 Cerami et al.55 https://www.cbioportal.org/
Oligonucleotides
Primer: TERTp forward:
5- TAATACGACTCACTATAGGGCAC
CCGTCCTGCCCCTTCACCTT-3′		 Koelsche et al.56 N/A
Primer: TERTp reverse:
5′- GTAAAACGACGGCCAGGGCTTCC
CACGTGCGCAGCAGGA-3′		 Koelsche et al.56 N/A
Software and algorithms
Cutadapt (v2.10) Martin et al.57 https://cutadapt.readthedocs.io/en/v2.10/index.html
FastQC Andrews et al.58 www.bioinformatics.babraham.ac.uk/projects/fastqc
Burrows-Wheeler Aligner (v0.7.17-r1188) Li et al.59 https://bio-bwa.sourceforge.net/
GATK v. 4.1.8.1 McKenna et al.60 https://gatk.broadinstitute.org/hc/en-us/sections/360009803432-4-1-8-1
STAR (v2.7.8a) Dobin et al.61 https://github.com/alexdobin/STAR
featureCounts (v2.0.2) Liao et al.62 https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts
DESeq2 (v1.30.1) Love et al.63 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
EnhancedVolcano (1.18) Blighe et al.64 https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
Heatmap3 Zhao et al.65 https://github.com/slzhao/heatmap3
GSEA (v4.1.0) Subramanian et al.66 https://www.gsea-msigdb.org/gsea/index.jsp
TIMER2.0 Li et al.67 http://timer.cistrome.org/
ggplot2 Wickham et al.68 https://ggplot2.tidyverse.org.
TIDE Jiang et al.47 http://tide.dfci.harvard.edu/
ComplexHeatmap Gu et al.69 https://github.com/jokergoo/ComplexHeatmap
STAR-Fusion (v2.7.8a) Hass et al.70 https://github.com/STAR-Fusion/STAR-Fusion/releases
Integrated Genomics Viewer Robinson et al.71 https://software.broadinstitute.org/software/igv/
Panther Thomas et al.72 https://pantherdb.org/
Seurat 4.0 Hao et al.73 https://satijalab.org/seurat/
SpaCET Ru et al.74 https://github.com/data2intelligence/SpaCET
maftools Mayakonda et al.75 https://github.com/PoisonAlien/maftools
brglm2 Kosmidis et al.76 https://github.com/ikosmidis/brglm2
Code for analysis and figure generation This paper https://doi.org/10.5281/zenodo.8229499