DNA Extraction:Article Title: Complete genome sequences of Brachyspira hyodysenteriae strains B204 and JR80.
Article Snippet: .. For DNA extraction, bacteria were grown anaerobically at 40°C for 22 h in Trypticase Soy broth (Oxoid, Wesel, Germany) with yeast extract (Oxoid, Wesel, Germany) (4), and DNA was extracted using the Wizard HMW DNA Extraction Kit (Promega, Walldorf, Germany) following the protocol for gram-negative bacteria. .. DNA quality was checked using a Bioanalyzer (Agilent).
Article Title: Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania
Article Snippet: The short-read sequencing was carried out using an Illumina machine (Hiseq X10 platform) according to the 250bp paired end protocol. .. For long read sequencing, DNA was extracted from blood isolates with the Fire Monkey Weight High molecular weight (HMW) genomic (gDNA) DNA Extraction Kit (Revolugen, UK) and the faecal isolates with the Wizard HMW DNA extraction kit (Promega, Wisconsin, USA). .. Library prep was carried out using the SQK-NBD114.24 Ligation Sequencing and Native Barcoding Kit according to the manufacturers protocol (Oxford Nanopore Technologies, Oxford, UK).
Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. The Wizard HMW DNA Extraction Kit (Promega, USA) was then used to extract DNA for long read sequencing according to the manufacturer’s protocol. .. Library preparation was performed at the Vienna Bio Center Core Facilities using the Multiplex Ligation Sequencing Kit and the Native Barcoding Kit (Oxford Nanopore Technologies, Oxford, UK).
Bacteria:Article Title: Complete genome sequences of Brachyspira hyodysenteriae strains B204 and JR80.
Article Snippet: .. For DNA extraction, bacteria were grown anaerobically at 40°C for 22 h in Trypticase Soy broth (Oxoid, Wesel, Germany) with yeast extract (Oxoid, Wesel, Germany) (4), and DNA was extracted using the Wizard HMW DNA Extraction Kit (Promega, Walldorf, Germany) following the protocol for gram-negative bacteria. .. DNA quality was checked using a Bioanalyzer (Agilent).
Sequencing:Article Title: Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania
Article Snippet: The short-read sequencing was carried out using an Illumina machine (Hiseq X10 platform) according to the 250bp paired end protocol. .. For long read sequencing, DNA was extracted from blood isolates with the Fire Monkey Weight High molecular weight (HMW) genomic (gDNA) DNA Extraction Kit (Revolugen, UK) and the faecal isolates with the Wizard HMW DNA extraction kit (Promega, Wisconsin, USA). .. Library prep was carried out using the SQK-NBD114.24 Ligation Sequencing and Native Barcoding Kit according to the manufacturers protocol (Oxford Nanopore Technologies, Oxford, UK).
Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. The Wizard HMW DNA Extraction Kit (Promega, USA) was then used to extract DNA for long read sequencing according to the manufacturer’s protocol. .. Library preparation was performed at the Vienna Bio Center Core Facilities using the Multiplex Ligation Sequencing Kit and the Native Barcoding Kit (Oxford Nanopore Technologies, Oxford, UK).
High Molecular Weight:Article Title: Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania
Article Snippet: The short-read sequencing was carried out using an Illumina machine (Hiseq X10 platform) according to the 250bp paired end protocol. .. For long read sequencing, DNA was extracted from blood isolates with the Fire Monkey Weight High molecular weight (HMW) genomic (gDNA) DNA Extraction Kit (Revolugen, UK) and the faecal isolates with the Wizard HMW DNA extraction kit (Promega, Wisconsin, USA). .. Library prep was carried out using the SQK-NBD114.24 Ligation Sequencing and Native Barcoding Kit according to the manufacturers protocol (Oxford Nanopore Technologies, Oxford, UK).
Extraction:
Recombinant:Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
Electron Microscopy:Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
Virus:Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
Produced:Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
Software:Article Title: The adaptation of chlamydiae to facultative host multicellularity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins 4′,6-diamidino-2-phenylindole (DAPI) Sigma-Aldrich Cat# D9542 Citifluor AF1 Electron Microscopy Sciences Cat# 17970-25 CellTracker Deep Red Thermo Fisher Scientific Cat# C34565 CellTracker Green CMFDA Thermo Fisher Scientific Cat# C7025 Critical commercial assays innuPREP DNA Mini Kit 2.0 IST Innuscreen 845-KS-1042010 QIAamp 96 Virus QIAcube HT Kit Qiagen Cat# 57731 Qubit dsDNA BR Assay Kit Qubit Cat# Q32850 QX200 ddPCR EvaGreen Supermix Bio-Rad Cat# 186-4034 Wizard HMW DNA Extraction Kit Promega Cat# A2920 Native Barcoding Kit 24 V14 Oxford nanopore technologies Cat# SQK-NBD110-24 NEBNext Ultra II FS DNA Library Prep Kit New England Biolabs Cat# E7805L Deposited data Reclusachlamydia socialis genome This study BioProject: PRJEB79376 18S rRNA Sequence of Dictyostelium giganteum PALH This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Concatenated protein alignment produced by CheckM This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Phylogenetic tree in Newick tree format This study Zenodo: https://doi.org/10.5281/zenodo.15527327 Experimental models: Organisms/strains Dictyostelium giganteum PALH This study NCBI: PRJEB79376 Klebsiella aerogenes Soldati Lab Dicty base: DBS0351098 Escherichia coli ECGRC Cat# JW5503-1 Acanthamoeba terricola ATCC Cat# 50373 Parachlamydia acanthamoebae UV7 ATCC Cat# VR-1476 Oligonucleotides Primer SigF2 (5’-CRGCGTGGATGAGGCAT-3’) Haider et al.108 N/A Primer SigR2 (5’-TCAGTCCCARTGTTGGC-3’) Haider et al.108 N/A Primer TAReuk454FWD (5′-CCAGCASCYGCGGTAATTCC-3′) Stoeck et al.109 N/A Primer TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) Stoeck et al.109 N/A Chla-282, 5’- CTC AAT CCG CCT AGA CGT -3’ Pizzetti et al.110 N/A Chls-523, 5’- CCTCCGTATTACCGCAGC -3’ Poppert et al.111 N/A Euk-516 (5’- GGA GGG CAA GTC TGG T -3’) Amann et al.112 N/A Software and algorithms FastQC v0.11.9 Andrews et al.113 https://github.com/s-andrews/FastQC Cutadapt 3.5 Martin114 https://github.com/marcelm/cutadapt Porechop v0.2.4 Wick et al.115 https://github.com/rrwick/Porechop Canu v2.0 Wick et al.116 https://github.com/marbl/canu Unicycler v0.4.8 Koren et al.117 https://github.com/rrwick/Unicycler Ori-finder 2022 Dong et al.118 https://tubic.org/Ori-Finder2022/ public/index.php/index Originx Worning et al.119 N/A (Continued on next page) ll OPEN ACCESS e1 Current Biology 35, 1–13.e1–e4, July 21, 2025 Article ..
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