KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| E. coli: Bl21 DE3 competent cells | NEB | Cat# C2527I |
| E. coli: DH5α competent cells | Thermo Fisher Scientific | Cat# 18265017 |
| Chemicals, peptides, and recombinant proteins | ||
| TCEP | Soltec | Cat# M115 |
| Protease inhibitor cocktail | Thermo Fisher Scientific | Cat# 1861278 |
| Q5 DNA Polymerase | NEB | Cat# M0491L |
| T4 Polynucleotide Kinase | NEB | Cat# M0201L |
| γ-32P ATP | PerkinElmer | Cat# NEG502A250UC |
| Desthiobiotin | Sigma-Aldrich | Cat# D1411 |
| Critical commercial assays | ||
| Gel DNA recovery kit | Zymo Research | Cat# D4008 |
| Oligonucleotides | ||
| Sense DNA to make a splayed prespacer substrate: [Alexa546]TACATGCTCTAGCAAAACGACTTGCACAACGAGG | Europhins | N/A |
| Anti-sense DNA to make a splayed prespacer substrate: AAATTAAGTGCAAGTCGTTTTGCTAGAGCTACAT | Europhins | N/A |
| Sense DNA to make a 40 bp prespacer substrate: TCTACATGGTCTAGGAAAAGGACTTGGACAAGGAGGTATA | Europhins | N/A |
| Anti-sense DNA to make a 40 bp prespacer substrate: TATACCTCCTTGTCCAAGTCCTTTTCCTAGACCATGTAGA | Europhins | N/A |
| Forward primer to make 32P-labelled CRISPR integration substrates: CCAATTGCCCGAAGCTTC | Europhins | N/A |
| Reverse primer to make 32P-labelled CRISPR integration substrates: TCCAGAAGTCACCACCCG | Europhins | N/A |
| Primer to amplify integration products, P1: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGACCACCCGGCTTTCTTAG | Europhins | N/A |
| Primer to amplify integration products, P2: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCAATTGCCCGAAGCTTC | Europhins | N/A |
| Primer to amplify integration products, P3: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTGGTCTAGGAAAAGGACTTGGAC | Europhins | N/A |
| Primer to amplify integration products, P4: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTCCTTGTCCAAGTCCTTTTCC | Europhins | N/A |
| Recombinant DNA | ||
| Plasmid: pCas1-2/3 | 25 | Addgene plasmid # 89240 |
| Plasmid: pHisIHFαIHFβ | This paper | Addgene plasmid # 149384 |
| Plasmid: pStrepIHFβ | This paper | Addgene plasmid # 149385 |
| Plasmid: pCRISPR2_wt | This paper | Addgene plasmid # 149386 |
| Plasmid: pCRISPR2_-6D | This paper | Addgene plasmid # 149387 |
| Plasmid: pCRISPR2_-5D | This paper | Addgene plasmid # 149388 |
| Plasmid: pCRISPR2_+1D | This paper | Addgene plasmid # 149389 |
| Plasmid: pCRISPR2_+5D | This paper | Addgene plasmid # 149390 |
| Plasmid: pCRISPR2_+10D | This paper | Addgene plasmid # 149391 |
| Plasmid: pCRISPR_+10D+7U | This paper | Addgene plasmid # 149393 |
| Plasmid: pCRISPR_+10D+10U | This paper | Addgene plasmid # 149394 |
| Plasmid: pCRISPR2_IHF_Opt | This paper | Addgene plasmid # 149395 |
| Plasmid: pCRISPR2_IHF_Mut | This paper | Addgene plasmid # 149396 |
| Plasmid: pCRISPR2_motif_scram | This paper | Addgene plasmid # 149397 |
| Plasmid: pCRISPR2_IHFdist_rm | This paper | Addgene plasmid # 162318 |
| Plasmid: pCRISPR2_IRdist_scram | This paper | Addgene plasmid # 162319 |
| Software and algorithms | ||
| MEME v5.3.3 | 64 | https://meme-suite.org/meme/tools/meme |
| FIMO v5.3.3 | 22 | https://meme-suite.org/meme/tools/fimo |
| WebLogo v3.7 | 65 | http://weblogo.threeplusone.com/create.cgi |
| 3D-DART | 61 | https://github.com/haddocking/3D-DART |
| Pymol v1.8.2.3 | Schrodinger | https://www.schrodinger.com/downloads/releases |
| ChimeraX v1.1 | UCSF | https://www.rbvi.ucsf.edu/chimerax/download.html |
| R-script for analysis of High-Throughput Sequencing data | This paper | https://github.com/WiedenheftLab/HTS_integration_analysis |
| Python script to extract leader sequences from CRISPRDetect output and perform phylogenetic analysis | This paper | https://github.com/WiedenheftLab/CRISPRleaderget |
| Python script to fetch sequences from a Multi-FASTA file by accession number | This paper | https://github.com/WiedenheftLab/seq_fetch |
| OriginPro | OriginLab | https://www.originlab.com/index.aspx?go=Products/Origin |
| CRISPRDetect v2.4 | 20 | https://github.com/davidchyou/CRISPRDetect_2.4 |
| RStudio | RStudio | https://www.rstudio.com/products/rstudio/ |
| MAFFT v7.429 | 69 | https://mafft.cbrc.jp/alignment/software/ |
| CD-HIT v4.8.1 | 67,68 | https://github.com/weizhongli/cdhit/releases/tag/V4.8.1 |
| MaxAlign v1.1 | 70 | https://services.healthtech.dtu.dk/service.php?MaxAlign-1.2 |
| FastTree v2.1.11 | 71 | http://www.microbesonline.org/fasttree/#Install |
| ggtree | 72–74 | https://github.com/YuLab-SMU/ggtree |
| ggplot2 | 75 | https://github.com/tidyverse/ggplot2 |
| PEAR | 78 | https://github.com/tseemann/PEAR |
| Other | ||
| Spin concentrators | Corning | Cat# 431491 |
| HisTrap HP resin | Cytiva | Cat# 17524701 |
| Microspin G25 columns | Cytiva | Cat# 27-5325-01 |
| HiLoad Superdex 200 26/600 pg | Cytiva | Cat# 28989336 |
| Superdex 75 10/300 GL | Cytiva | Cat# 17-5174-01 |
| HiTrap Heparin HP resin | Cytiva | Cat# 17040701 |
| StrepTrap HP resin | Cytiva | Cat# 28907546 |