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. 2021 Aug 30;1(1):100001. doi: 10.1016/j.xgen.2021.100001
REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and virus strains
NEB Stable Cells New England Biolabs Cat#C3040I
Oligonucleotides
lncRNA-targeting gRNA oligo sequences, see Table S2 This paper N/A
qPCR primers for gene expression quantification, see Table S3 This paper N/A
Chemicals, peptides, and recombinant proteins
Polyethyleneimine Polysciences Cat#23966
Critical commercial assays
Direct-zol RNA MicroPrep Zymo Research Cat# R2061
RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat# K1691
Luna Universal qPCR Master Mix New England Biolabs Cat#M3003E
Deposited data
Reference transcriptome (H. sapiens: GENCODE v19, GRCh37) ENSEMBL ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.pc_transcripts.fa.gz
Reference annotations (H. sapiens: GENCODE v19, GRCh37) ENSEMBL ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
Reference transcriptome (M. musculus: GENCODE M24, mm10) ENSEMBL ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24/gencode.vM24.pc_transcripts.fa.gz
Reference annotations (M. musculus: GENCODE M24, mm10) ENSEMBL ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24/gencode.vM24.annotation.gtf.gz
Reference transcriptome - mRNA (D. rerio: Ensembl v99, GRCz11) ENSEMBL ftp://ftp.ensembl.org/pub/release-99/fasta/danio_rerio/cdna/Danio_rerio.GRCz11.cdna.all.fa.gz
Reference transcriptome - ncRNA (D. rerio: Ensembl v99, GRCz11) ENSEMBL ftp://ftp.ensembl.org/pub/release-99/fasta/danio_rerio/ncrna/Danio_rerio.GRCz11.ncrna.fa.gz
Reference annotations (D. rerio: Ensembl v99, GRCz11) ENSEMBL ftp://ftp.ensembl.org/pub/release-99/gtf/danio_rerio/Danio_rerio.GRCz11.99.gtf.gz
Reference transcriptome - mRNA (D. melanogaster: Ensembl v99, BDGP6) ENSEMBL ftp://ftp.ensembl.org/pub/release-100/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.28.cdna.all.fa.gz
Reference transcriptome - ncRNA (D. melanogaster: Ensembl v99, BDGP6) ENSEMBL ftp://ftp.ensembl.org/pub/release-99/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.28.ncrna.fa.gz
Reference annotations (D. melanogaster: Ensembl v99, BDGP6) ENSEMBL ftp://ftp.ensembl.org/pub/release-100/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.28.100.gtf.gz
Reference transcriptome - mRNA (C. elegans: Ensembl Plants v46, WBcel235) ENSEMBL ftp://ftp.ensembl.org/pub/release-100/fasta/caenorhabditis_elegans/cdna/Caenorhabditis_elegans.WBcel235.cdna.all.fa.gz
Reference transcriptome - ncRNA (C. elegans: Ensembl Plants v46, WBcel235) ENSEMBL ftp://ftp.ensembl.org/pub/release-99/fasta/caenorhabditis_elegans/ncrna/Caenorhabditis_elegans.WBcel235.ncrna.fa.gz
Reference annotations (C. elegans: Ensembl Plants v46, WBcel235) ENSEMBL ftp://ftp.ensembl.org/pub/release-100/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.100.gtf.gz
Reference transcriptome - mRNA (A. thaliana: Ensembl v99, TAIR10) ENSEMBL ftp://ftp.ensemblgenomes.org/pub/plants/release-46/fasta/arabidopsis_thaliana/cdna/Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz
Reference transcriptome - ncRNA (A. thaliana: Ensembl v99, TAIR10) ENSEMBL ftp://ftp.ensemblgenomes.org/pub/plants/release-46/fasta/arabidopsis_thaliana/ncrna/Arabidopsis_thaliana.TAIR10.ncrna.fa.gz
Reference annotations (A. thaliana: Ensembl v99, TAIR10) ENSEMBL ftp://ftp.ensemblgenomes.org/pub/plants/release-46/gff3/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.46.gff3.gz
Reference genome (SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2) NCBI https://www.ncbi.nlm.nih.gov/nuccore/1834374999
Reference annotation (SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2) NCBI https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2
Reference genome (MERS: Middle East respiratory syndrome coronavirus, complete genome) NCBI https://www.ncbi.nlm.nih.gov/nuccore/NC_019843.3
Reference annotation (MERS: Middle East respiratory syndrome coronavirus, complete genome) NCBI https://www.ncbi.nlm.nih.gov/nuccore/NC_019843.3
Reference genome (HIV1: Human immunodeficiency virus 1, complete genome) NCBI https://www.ncbi.nlm.nih.gov/nuccore/NC_001802.1
Reference annotation (HIV1: Human immunodeficiency virus 1, complete genome) NCBI https://www.ncbi.nlm.nih.gov/nuccore/NC_001802.1
Reference genome (H1N1: Influenza A virus) NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=641809
Reference annotation (H1N1: Influenza A virus) NCBI https://www.ncbi.nlm.nih.gov/nuccore/?term=Influenza+A+virus+(A%2FCalifornia%2F07%2F2009(H1N1))
Analyses and summary statistics of designed guide RNAs This paper https://gitlab.com/sanjanalab/cas13_webtool
Experimental models: Cell lines
HAP1 Landau lab N/A
NIH 3T3 ATCC CRL-1658
HAP1-Cas13d This study N/A
NIH 3T3-Cas13d This study N/A
HEK293FT Thermo Fisher Scientific Cat#R70007
Recombinant DNA
pLentiRNACRISPR_007 - TetO-NLS-RfxCas13d-NLS-WPRE-EFS-rtTA3-2A-Blast Wessels et al.14 Addgene 138149
pLentiRNAGuide_001 - hU6-RfxCas13d-DR1-BsmBI-EFS-Puro-WPRE Wessels et al.14 Addgene 138150
pMD2.G Trono Lab packaging and envelope plasmids Addgene 12259
psPAX2 Trono Lab packaging and envelope plasmids Addgene 12260
Software and algorithms
GraphPad Prism 8 GraphPad https://www.graphpad.com/
RStudio RStudio https://www.rstudio.com/
Python version 2.7.8 Python Software Foundation https://www.python.org
Cas13 guide design algorithm Wessels et al.14 https://gitlab.com/sanjanalab/cas13
Cas13 design tool This paper https://cas13design.nygenome.org/