Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| AD9 | This paper | SRR14131380 |
| AD10 | This paper | SRR14131379 |
| AD11 | This paper | SRR14131378 |
| AD12 | This paper | SRR14131376 |
| AD24 | This paper | SRR14131383 |
| AD25 | This paper | SRR14131382 |
| AD26 | This paper | SRR14131381 |
| AD30 | This paper | SRR14131374 |
| AD31 | This paper | SRR14131373 |
| AD32 | This paper | SRR14131372 |
| AD33 | This paper | SRR14131389 |
| AD34 | This paper | SRR14131387 |
| AD35 | This paper | SRR14131386 |
| AD36 | This paper | SRR14131385 |
| AD37 | This paper | SRR14131384 |
| AD38 | This paper | SRR14131400 |
| AD39 | This paper | SRR14131399 |
| AD40 | This paper | SRR14131388 |
| AD41 | This paper | SRR14131377 |
| AD42 | This paper | SRR14131375 |
| AD48 | This paper | SRR16077561 |
| AD49 | This paper | SRR16077560 |
| Chemicals, peptides, and recombinant proteins | ||
| Ampicillin | Nova Plus | Cat#0781-9408-80 |
| Vancomycin hydrochloride | Fisher Scientific | Cat#J62790.06 |
| Neomycin sulfate hydrate | Fisher Scientific | Cat#J61499.14 |
| Dextran Sulfate Sodium Salt | Fisher Scientific | Cat#AAJ6278722 |
| LB broth, Miller | Fisher Scientific | Cat#BP1426-500 |
| Critical commercial assays | ||
| MacConkey agar II | Fisher Scientific | Cat#B21172X |
| BIOLOG PM1 plates | Fisher Scientific | Cat#NC9040419 |
| BIOLOG PM2A plates | Fisher Scientific | Cat#NC0058821 |
| QIAamp Fast DNA Stool Kit | Qiagen | Cat#51604 |
| Quant-iT dsDNA Assay Kit, High Sensitivity | Invitrogen | Cat#Q33120 |
| Nextera XT DNA Library preparation kit | Illumina | Cat#FC-131-1096 |
| MiSeq Reagent Kit v3 | Illumina | Cat#15043895 |
| Deposited data | ||
| Liao et al. (2021); Yan et al. (2022) | SRA | PRJNA394877, PRJNA607574, PRJNA606262, PRJNA548153, PRJNA545312 |
| Genomes of the isolates reported in this paper | This paper | PRJNA545312; PRJNA606262; PRJNA607574 |
| Genome of Klebsiella sp. Kd70 TUC-EEAOC | SRA | PRJNA285494 |
| Genome of Klebsiella michiganensis strain ARO112 | SRA | PRJNA590204 |
| Genome of Klebsiella oxytoca strain CAV1374 | SRA | PRJNA246471 |
| Genome of Klebsiella oxytoca KCTC 1686 | SRA | PRJNA65523 |
| Genome of K. pneumoniae subsp. pneumoniae HS11286 | SRA | PRJNA84387 |
| Genome of K. michiganensis DSM25444 | SRA | PRJNA388837 |
| Genome of K. grimontii 06D021 | SRA | PRJEB21765 |
| Genome of K. oxytoca DSM5175 | SRA | PRJNA543274 |
| Genome of E. coli ATCC11775 | SRA | PRJNA472652 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL6/J | The Jackson Laboratory | JAX Cat#000664; RRID: IMSR_JAX:000664; Room #EM03 |
| Oligonucleotides | ||
| PCR for Sanger sequencing: 16S Forward 27F 5’-AGAGTTTGATCMTGGCTCAG-3’ | IDT | N/A |
| PCR for Sanger sequencing: 16S Reverse 803R 5’-CTACCRGGGTATCTAATCC-3’ | IDT | N/A |
| Software and algorithms | ||
| TaxUMAP | This paper | https://github.com/jsjse/taxumap; DOI: 10.5281/zenodo.7958500 |
| Python v3.7.9 | Python | python.org |
| Matlab v2020a | Matlab | https://www.mathworks.com/products/matlab.html |
| Bhatt lab workflow for the genomes’ assembly | Siranosian et al., 2022 | github.com/bhattlab/bhattlab_workflows |
| PATRIC Comprehensive Genome Analysis Tool | Wattam et al., 2017 | https://www.bvbrc.org/app/ComprehensiveGenomeAnalysis |
| Prokka | Seemann, 2014 | https://github.com/tseemann/prokka |
| Roary | Page et al., 2015 | https://github.com/sanger-pathogens/Roary |
| FastTree2 | Price et al., 2010 | http://www.microbesonline.org/fasttree/ |
| LIFE SCIENCE TABLE WITH EXAMPLES FOR AUTHOR REFERENCE | ||
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| Antibodies | ||
| Rabbit monoclonal anti-Snail | Cell Signaling Technology | Cat#3879S; RRID: AB 2255011 |
| Mouse monoclonal anti-Tubulin (clone DM1A) | Sigma-Aldrich | Cat#T9026; RRID: AB 477593 |
| Rabbit polyclonal anti-BMAL1 | This paper | N/A |
| Bacterial and virus strains | ||
| pAAV-hSyn-DIO-hM3D(Gq)-mCherry | Krashes et al.1 | Addgene AAV5; 44361-AAV5 |
| AAV5-EF1a-DIO-hChR2(H134R)-EYFP | Hope Center Viral Vectors Core | N/A |
| Cowpox virus Brighton Red | BEI Resources | NR-88 |
| Zika-SMGC-1, GENBANK: KX266255 | Isolated from patient (Wang et al.2) | N/A |
| Staphylococcus aureus | ATCC | ATCC 29213 |
| Streptococcus pyogenes: M1 serotype strain: strain SF370; M1 GAS | ATCC | ATCC 700294 |
| Biological samples | ||
| Healthy adult BA9 brain tissue | University of Maryland Brain & Tissue Bank; http://medschool.umaryland.edu/btbank/ | Cat#UMB1455 |
| Human hippocampal brain blocks | New York Brain Bank | http://nybb.hs.columbia.edu/ |
| Patient-derived xenografts (PDX) | Children's Oncology Group Cell Culture and Xenograft Repository | http://cogcell.org/ |
| Chemicals, peptides, and recombinant proteins | ||
| MK-2206 AKT inhibitor | Selleck Chemicals | S1078; CAS: 1032350-13-2 |
| SB-505124 | Sigma-Aldrich | S4696; CAS: 694433-59-5 (free base) |
| Picrotoxin | Sigma-Aldrich | P1675; CAS: 124-87-8 |
| Human TGF-β | R&D | 240-B; GenPept: P01137 |
| Activated S6K1 | Millipore | Cat#14-486 |
| GST-BMAL1 | Novus | Cat#H00000406-P01 |
| Critical commercial assays | ||
| EasyTag EXPRESS 35S Protein Labeling Kit | PerkinElmer | NEG772014MC |
| CaspaseGlo 3/7 | Promega | G8090 |
| TruSeq ChIP Sample Prep Kit | Illumina | IP-202-1012 |
| Deposited data | ||
| Raw and analyzed data | This paper | GEO: GSE63473 |
| B-RAF RBD (apo) structure | This paper | PDB: 5J17 |
| Human reference genome NCBI build 37, GRCh37 | Genome Reference Consortium | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| Nanog STILT inference | This paper; Mendeley Data | http://dx.doi.org/10.17632/wx6s4mj7s8.2 |
| Affinity-based mass spectrometry performed with 57 genes | This paper; Mendeley Data | Table S8; http://dx.doi.org/10.17632/5hvpvspw82.1 |
| Experimental models: Cell lines | ||
| Hamster: CHO cells | ATCC | CRL-11268 |
| D. melanogaster: Cell line S2: S2-DRSC | Laboratory of Norbert Perrimon | FlyBase: FBtc0000181 |
| Human: Passage 40 H9 ES cells | MSKCC stem cell core facility | N/A |
| Human: HUES 8 hESC line (NIH approval number NIHhESC-09-0021) | HSCI iPS Core | hES Cell Line: HUES-8 |
| Experimental models: Organisms/strains | ||
| C. elegans: Strain BC4011: srl-1(s2500) II; dpy-18(e364) III; unc-46(e177)rol-3(s1040) V. | Caenorhabditis Genetics Center | WB Strain: BC4011; WormBase: WBVar00241916 |
| D. melanogaster: RNAi of Sxl: y[1] sc[*] v[1]; P{TRiP.HMS00609}attP2 | Bloomington Drosophila Stock Center | BDSC:34393; FlyBase: FBtp0064874 |
| S. cerevisiae: Strain background: W303 | ATCC | ATTC: 208353 |
| Mouse: R6/2: B6CBA-Tg(HDexon1)62Gpb/3J | The Jackson Laboratory | JAX: 006494 |
| Mouse: OXTRfl/fl: B6.129(SJL)-Oxtrtm1.1Wsy/J | The Jackson Laboratory | RRID: IMSR_JAX:008471 |
| Zebrafish: Tg(Shha:GFP)t10: t10Tg | Neumann and Nuesslein-Volhard3 | ZFIN: ZDB-GENO-060207-1 |
| Arabidopsis: 35S::PIF4-YFP, BZR1-CFP | Wang et al.4 | N/A |
| Arabidopsis: JYB1021.2: pS24(AT5G58010)::cS24:GFP(-G):NOS #1 | NASC | NASC ID: N70450 |
| Oligonucleotides | ||
| siRNA targeting sequence: PIP5K I alpha #1: ACACAGUACUCAGUUGAUA | This paper | N/A |
| Primers for XX, see Table SX | This paper | N/A |
| Primer: GFP/YFP/CFP Forward: GCACGACTTCTTCAAGTCCGCCATGCC | This paper | N/A |
| Morpholino: MO-pax2a GGTCTGCTTTGCAGTGAATATCCAT | Gene Tools | ZFIN: ZDB-MRPHLNO-061106-5 |
| ACTB (hs01060665_g1) | Life Technologies | Cat#4331182 |
| RNA sequence: hnRNPA1_ligand: UAGGGACUUAGGGUUCUCUCUAGGGACUUAGGGUUCUCUCUAGGGA | This paper | N/A |
| Recombinant DNA | ||
| pLVX-Tight-Puro (TetOn) | Clonetech | Cat#632162 |
| Plasmid: GFP-Nito | This paper | N/A |
| cDNA GH111110 | Drosophila Genomics Resource Center | DGRC:5666; FlyBase:FBcl0130415 |
| AAV2/1-hsyn-GCaMP6- WPRE | Chen et al.5 | N/A |
| Mouse raptor: pLKO mouse shRNA 1 raptor | Thoreen et al.6 | Addgene Plasmid #21339 |
| Software and algorithms | ||
| ImageJ | Schneider et al.7 | https://imagej.nih.gov/ij/ |
| Bowtie2 | Langmead and Salzberg8 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools | Li et al.9 | http://samtools.sourceforge.net/ |
| Weighted Maximal Information Component Analysis v0.9 | Rau et al.10 | https://github.com/ChristophRau/wMICA |
| ICS algorithm | This paper; Mendeley Data | http://dx.doi.org/10.17632/5hvpvspw82.1 |
| Other | ||
| Sequence data, analyses, and resources related to the ultra-deep sequencing of the AML31 tumor, relapse, and matched normal | This paper | http://aml31.genome.wustl.edu |
| Resource website for the AML31 publication | This paper | https://github.com/chrisamiller/aml31SuppSite |
| PHYSICAL SCIENCE TABLE WITH EXAMPLES FOR AUTHOR REFERENCE | ||
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| Chemicals, peptides, and recombinant proteins | ||
| QD605 streptavidin conjugated quantum dot | Thermo Fisher Scientific | Cat#Q10101MP |
| Platinum black | Sigma-Aldrich | Cat#205915 |
| Sodium formate BioUltra, ≥99.0% (NT) | Sigma-Aldrich | Cat#71359 |
| Chloramphenicol | Sigma-Aldrich | Cat#C0378 |
| Carbon dioxide (13C, 99%) (<2% 18O) | Cambridge Isotope Laboratories | CLM-185-5 |
| Poly(vinylidene fluoride-co-hexafluoropropylene) | Sigma-Aldrich | 427179 |
| PTFE Hydrophilic Membrane Filters, 0.22 μm, 90 mm | Scientificfilters.com/TischScientific | SF13842 |
| Critical commercial assays | ||
| Folic Acid (FA) ELISA kit | Alpha Diagnostic International | Cat# 0365-0B9 |
| TMT10plex Isobaric Label Reagent Set | Thermo Fisher | A37725 |
| Surface Plasmon Resonance CM5 kit | GE Healthcare | Cat#29104988 |
| NanoBRET Target Engagement K-5 kit | Promega | Cat#N2500 |
| Deposited data | ||
| B-RAF RBD (apo) structure | This paper | PDB: 5J17 |
| Structure of compound 5 | This paper; Cambridge Crystallographic Data Center | CCDC: 2016466 |
| Code for constraints-based modeling and analysis of autotrophic E. coli | This paper | https://gitlab.com/elad.noor/sloppy/tree/master/rubisco |
| Software and algorithms | ||
| Gaussian09 | Frish et al.1 | https://gaussian.com |
| Python version 2.7 | Python Software Foundation | https://www.python.org |
| ChemDraw Professional 18.0 | PerkinElmer | https://www.perkinelmer.com/category/chemdraw |
| Weighted Maximal Information Component Analysis v0.9 | Rau et al.2 | https://github.com/ChristophRau/wMICA |
| Other | ||
| DASGIP MX4/4 Gas Mixing Module for 4 Vessels with a Mass Flow Controller | Eppendorf | Cat#76DGMX44 |
| Agilent 1200 series HPLC | Agilent Technologies | https://www.agilent.com/en/products/liquid-chromatography |
| PHI Quantera II XPS | ULVAC-PHI, Inc. | https://www.ulvacphi.com/en/products/xps/phi-quantera-ii/ |