DNA Extraction:Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
DNA Purification:Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
DNA Library Preparation:Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
Software:Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
Article Title: Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Master-Pure DNA extraction kit Epicentre, Madison, USA Catalog No. 12888-50 DNA Purification Kit Macherey-Nagel, Duren, Germany Catalog No. MC89010 NexteraXT DNA Library Preparation Kit Illumina, California, USA FC-131-1096 Deposited Data A newly sequenced cohort from Spain: MAMI cohort This study ENA: PRJEB74322 Software and Algorithms Trim Galore v0.6.6 https://github.com/FelixKrueger/ TrimGalore https://github.com/FelixKrueger/TrimGalore Bowtie2 v2.3.4.3 Langmead and Salzberg70 https://github.com/BenLangmead/bowtie2 MetaPhlAn v3.0.7 + database v30_ CHOCOPhlAn_201901 Beghini et al.29 https://github.com/biobakery/MetaPhlAn StrainPhlAn 3 Beghini et al.29 https://github.com/biobakery/MetaPhlAn PanPhlAn 3 + Bifidobacterium longum Pangenome Beghini et al.29 https://github.com/biobakery/MetaPhlAn CAZy database CAZyDB_07312020 Yin et al.71 https://bcb.unl.edu/dbCAN2/download/ DIAMOND v2.0.8 Buchfink et al.72 https://github.com/bbuchfink/diamond R package cutpointr v1.1.2 Thiele73 https://github.com/Thie1e/cutpointr R package rstatix v0.7.2 Kassambara74 https://github.com/kassambara/rstatix R package dunn.test v1.6.5 Dinno et al.75 https://github.com/cran/dunn.test R package ggsignif v0.6.4 Ahlmann-Eltze and Patil76 https://github.com/const-ae/ggsignif R package cowplot v1.1.1 Wilke77 https://github.com/wilkelab/cowplot R package ComplexHeatmap 2.12.1 Gu et al.78,79 https://github.com/jokergoo/ComplexHeatmap R package vegan 2.6-4 Oksanen et al.80 https://github.com/vegandevs/vegan R package ggplot2 3.4.1 Wickham81 https://github.com/tidyverse/ggplot2 ..
Sequencing:Article Title: Evaluation of high-throughput sequencing for replacing the conventional adventitious virus detection assays used for biologics.
Article Snippet: Sequencing of fourteen samples was conducted in two runs of Illumina NovaSeq 6000 (seven samples for each run) using the NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) - (Cat # 20028314, Illumina). .. Library sequencing was performed using the following parameters: 2 × 151 cycles paired-end sequencing (according to Illumina’s instructions), pooled library at 1 nM each and PhiX Control v3 Library (1% v/v of pool library spiked) - (Catalogue no. FC-110-3001, Illumina). .. Demultiplexing of sequencing was performed using the Illumina tool bcl2fastq (v. 2.19.1.403) 49.
Article Title: RNA printing and sequencing devices, methods, and systems
Article Snippet: .. Amplification and Sequencing of Tagmented cDNA Purified product from each of the small piece was tagmented, barcoded, and amplified using a commercially available kit (Nextera XT, FC-131-1024, Illumina) per the vendor's instructions with the following modifications. ..
Control:Article Title: Evaluation of high-throughput sequencing for replacing the conventional adventitious virus detection assays used for biologics.
Article Snippet: Sequencing of fourteen samples was conducted in two runs of Illumina NovaSeq 6000 (seven samples for each run) using the NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) - (Cat # 20028314, Illumina). .. Library sequencing was performed using the following parameters: 2 × 151 cycles paired-end sequencing (according to Illumina’s instructions), pooled library at 1 nM each and PhiX Control v3 Library (1% v/v of pool library spiked) - (Catalogue no. FC-110-3001, Illumina). .. Demultiplexing of sequencing was performed using the Illumina tool bcl2fastq (v. 2.19.1.403) 49.
Amplification:Article Title: RNA printing and sequencing devices, methods, and systems
Article Snippet: .. Amplification and Sequencing of Tagmented cDNA Purified product from each of the small piece was tagmented, barcoded, and amplified using a commercially available kit (Nextera XT, FC-131-1024, Illumina) per the vendor's instructions with the following modifications. ..
Purification:Article Title: RNA printing and sequencing devices, methods, and systems
Article Snippet: .. Amplification and Sequencing of Tagmented cDNA Purified product from each of the small piece was tagmented, barcoded, and amplified using a commercially available kit (Nextera XT, FC-131-1024, Illumina) per the vendor's instructions with the following modifications. ..
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