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. 2022 Jun 21;11:e77999. doi: 10.7554/eLife.77999

Appendix 1—key resources table.

Reagent type (species) or resource Designation Source or reference Identifiers Additional information
gene (Danio rerio) serpine3 Ensembl ENSDART00000132915.2
gene (Homo sapiens) SERPINE3 Ensembl ENST00000524365
strain, strain background (Danio rerio) WT (AB) Zebrafish International Resource Center
strain, strain background (Mus musculus) WT (C57BL/6JOlaHsd) Envigio
genetic reagent (Danio rerio) cbg17 This paper See Materials and Methods “Generation of KO lines and genotyping”
genetic reagent (Danio rerio) cbg18 This paper See Materials and Methods “Generation of KO lines and genotyping”
Antibody Anti-digoxigenin-AP (polyclonal sheep) Sigma-Aldrich Cat. #: 11093274910, RRID: AB_2734716 IF (1:4000)
Antibody Anti-digoxigenin-POD conjugated (polyclonal sheep) Roche Cat. #: 11207733910, RRID: AB_514500 IF (1:500)
Antibody Anti-gfap ZRF-1 (monoclonal mouse) Zebrafish International Resource Center Cat. #: zrf-1, RRID: AB_10013806 IF (1:200)
antibody Anti-choline acetyltransferase (polyclonal goat) Sigma-Aldrich Millipore Cat. #: AB144P, RRID: AB_2079751 IF (1:500)
antibody Anti-protein kinase C alpha (polyclonal rabbit) Santa Cruz Biotechnology Cat. #: sc-208, RRID: AB_2168668 IF (1:500)
antibody Anti-goat lgG (H+L) Alexa 488 (polyclonal chicken) Invitrogen Cat. #: A21467 IF (1:750)
antibody Anti-rabbit lgG (H+L) Alexa 488 (polyclonal goat) Invitrogen Cat. #: A11034 IF (1:750)
recombinant DNA reagent serpine3-pCRII-topo vector This paper See Materials and Methods “Generation of KO lines and genotyping”
sequence-based reagent Zf_serp_F This paper qPCR primer GAGACCCAAAACCTGCCCTT
sequence-based reagent Zf_serp_R This paper qPCR primer AGCCGGAAATGACCGATATTGA
sequence-based reagent Mm_serp_F This paper qPCR primer TGGAGCTTTCAGAGGAGGGTA
sequence-based reagent Mm_serp_R This paper qPCR primer GATACTGAAGACAAACCCTGTGC
sequence-based reagent Zf_rpl13a_F https://doi.org/10.1111/j.1745-7270.2007.00283.x qPCR primer TCTGGAGGAACTGTAAGAGGTATGC
sequence-based reagent Zf_rpl13a_R https://doi.org/10.1111.i.1745-7270.2007.00283.x qPCR primer AGACGCACAATCTTGAGAGCGA
sequence-based reagent Zf_actb_F https://doi.org/10.1007/s00441-020-03318-2 qPCR primer CGAGCAGGAGATGGGAACC
sequence-based reagent Zf_actb_R https://doi.org/10.1007/s00441-020-03318-2 qPCR primer CAACGGAAACGCTCATTGC
sequence-based reagent Mm_Rpl27_F This paper qPCR primer TTGAGGAGCGATACAAGACAGG
sequence-based reagent Mm_Rpl27_R This paper qPCR primer CCCAGTCTCTTCCCACACAAA
sequence-based reagent Guide1 This paper Crispr guide GGTATTTGTACTCTAATGAA
sequence-based reagent Guide2 This paper Crispr guide TGTACTCTAATGAAAGGAAC
sequence-based reagent Guide3 This paper Crispr guide CTCACACAGGACAATCCGGCAGG
sequence-based reagent Guide4 This paper Crispr guide TCTTCTGCAACTCGGGGCCA
sequence-based reagent Guide5 This paper Crispr guide TCTCTGTGAGCGTCTGGTAG
sequence-based reagent Guide6 This paper Crispr guide AACACTCTGGTTCAGCTCGA
sequence-based reagent For1 This paper Genotyping primer GAAATCGCATGTCACGCAGAAAT
sequence-based reagent Rev2 This paper Genotyping primer ATATCGGAACTGACATACTGAACG
sequence-based reagent Rev2.2 This paper Genotyping primer GTGAGCTTCGTGTTTGTGGT
sequence-based reagent For3 This paper Genotyping primer GGCATTGTTGAGATTCAGTAGTCA
sequence-based reagent Rev4 This paper Genotyping primer CAGTTTACTCCTACCATTGACATC
peptide, recombinant protein Alt-R CRISPR-Cas 9 Nuclease IDT Cat. #: 10000735
commercial assay or kit RNeasy mini kit Qiagen Cat. #: 74,106
commercial assay or kit RNeasy midi kit Qiagen Cat. #: 75,144
commercial assay or kit ProtoScript II First Strand Synthesis kit NEB Cat. #: E6560S
commercial assay or kit TSA Plus Cy3/Cy5 kit Perkin-Elmer Cat. #: NEL744001KT
commercial assay or kit Alt-R CRISPR-Cas9 tracr RNA IDT Cat. #: 1072532
software, algorithm Enrichr https://doi.org/10.1093/nar/gkw377 RRID:SCR_001575
software, algorithm TOGA Kirilenko et al., titled 'Integrating gene annotation with orthology inference at scale', under review (https://github.com/hillerlab/TOGA; Kirilenko and Hiller, 2022)
software, algorithm CESAR 2.0 https://doi.org/10.1093/bioinformatics/btx527
software, algorithm RELAX https://doi.org/10.1093/molbev/msu400 RRID:SCR_016162
software, algorithm MACSE v2.0 https://doi.org/10.1093/molbev/msy159
software, algorithm Jalview https://doi.org/10.1093/molbev/msy159 RRID:SCR_006459
software, algorithm Human protein atlas https://doi.org/10.1038/nbt1210-1248 RRID:SCR_006710
software, algorithm Gene Expression Atlas https://doi.org/10.1093/nar/gkz947 RRID:SCR_007989
software, algorithm PyMOL Schrödinger and DeLano, 2020
RRID:SCR_000305
software, algorithm Fiji https://doi.org/10.1038/nmeth.2019 RRID:SCR_002285
software, algorithm R Other RRID:SCR_001905 https://cran.r-project.org/src/base/R-3/
software, algorithm ggplot2 Other RRID:SCR_014601 http://docs.ggplot2.org/current/
software, algorithm tseries Other https://CRAN.R-project.org/package=tseries
software, algorithm effsize Other https://cran.r-project.org/web/packages/effsize/index.html
software, algorithm SignalP5 https://doi.org/10.1038/s41587-019-0036-z
software, algorithm DeepLoc https://doi.org/10.1093/bioinformatics/btx431
software, algorithm ChopChop v2 https://doi.org/10.1093/nar/gkw398 RRID:SCR_015723