Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis

Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial s...
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Autor*in:	Hammond, Maria [verfasserIn] Homa, Felix [verfasserIn] Andersson-Svahn, Helene [verfasserIn] Ettema, Thijs J. G. [verfasserIn] Joensson, Haakan N. [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2016

Schlagwörter:	Whole genome amplification Multiple displacement amplification Metagenomics Droplet microfluidics Amplification bias

Übergeordnetes Werk:	Enthalten in: Microbiome - London : Biomed Central, 2013, 4(2016), 1 vom: 06. Okt.
Übergeordnetes Werk:	volume:4 ; year:2016 ; number:1 ; day:06 ; month:10

Links:	Volltext

DOI / URN:	10.1186/s40168-016-0197-7

Katalog-ID:	SPR033229295

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520			\|a Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.
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allfields	10.1186/s40168-016-0197-7 doi (DE-627)SPR033229295 (SPR)s40168-016-0197-7-e DE-627 ger DE-627 rakwb eng 570 ASE Hammond, Maria verfasserin aut Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA. Whole genome amplification (dpeaa)DE-He213 Multiple displacement amplification (dpeaa)DE-He213 Metagenomics (dpeaa)DE-He213 Droplet microfluidics (dpeaa)DE-He213 Amplification bias (dpeaa)DE-He213 Homa, Felix verfasserin aut Andersson-Svahn, Helene verfasserin aut Ettema, Thijs J. G. verfasserin aut Joensson, Haakan N. verfasserin aut Enthalten in Microbiome London : Biomed Central, 2013 4(2016), 1 vom: 06. Okt. (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:4 year:2016 number:1 day:06 month:10 https://dx.doi.org/10.1186/s40168-016-0197-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2016 1 06 10
spelling	10.1186/s40168-016-0197-7 doi (DE-627)SPR033229295 (SPR)s40168-016-0197-7-e DE-627 ger DE-627 rakwb eng 570 ASE Hammond, Maria verfasserin aut Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA. Whole genome amplification (dpeaa)DE-He213 Multiple displacement amplification (dpeaa)DE-He213 Metagenomics (dpeaa)DE-He213 Droplet microfluidics (dpeaa)DE-He213 Amplification bias (dpeaa)DE-He213 Homa, Felix verfasserin aut Andersson-Svahn, Helene verfasserin aut Ettema, Thijs J. G. verfasserin aut Joensson, Haakan N. verfasserin aut Enthalten in Microbiome London : Biomed Central, 2013 4(2016), 1 vom: 06. Okt. (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:4 year:2016 number:1 day:06 month:10 https://dx.doi.org/10.1186/s40168-016-0197-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2016 1 06 10
allfields_unstemmed	10.1186/s40168-016-0197-7 doi (DE-627)SPR033229295 (SPR)s40168-016-0197-7-e DE-627 ger DE-627 rakwb eng 570 ASE Hammond, Maria verfasserin aut Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA. Whole genome amplification (dpeaa)DE-He213 Multiple displacement amplification (dpeaa)DE-He213 Metagenomics (dpeaa)DE-He213 Droplet microfluidics (dpeaa)DE-He213 Amplification bias (dpeaa)DE-He213 Homa, Felix verfasserin aut Andersson-Svahn, Helene verfasserin aut Ettema, Thijs J. G. verfasserin aut Joensson, Haakan N. verfasserin aut Enthalten in Microbiome London : Biomed Central, 2013 4(2016), 1 vom: 06. Okt. (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:4 year:2016 number:1 day:06 month:10 https://dx.doi.org/10.1186/s40168-016-0197-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2016 1 06 10
allfieldsGer	10.1186/s40168-016-0197-7 doi (DE-627)SPR033229295 (SPR)s40168-016-0197-7-e DE-627 ger DE-627 rakwb eng 570 ASE Hammond, Maria verfasserin aut Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA. Whole genome amplification (dpeaa)DE-He213 Multiple displacement amplification (dpeaa)DE-He213 Metagenomics (dpeaa)DE-He213 Droplet microfluidics (dpeaa)DE-He213 Amplification bias (dpeaa)DE-He213 Homa, Felix verfasserin aut Andersson-Svahn, Helene verfasserin aut Ettema, Thijs J. G. verfasserin aut Joensson, Haakan N. verfasserin aut Enthalten in Microbiome London : Biomed Central, 2013 4(2016), 1 vom: 06. Okt. (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:4 year:2016 number:1 day:06 month:10 https://dx.doi.org/10.1186/s40168-016-0197-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2016 1 06 10
allfieldsSound	10.1186/s40168-016-0197-7 doi (DE-627)SPR033229295 (SPR)s40168-016-0197-7-e DE-627 ger DE-627 rakwb eng 570 ASE Hammond, Maria verfasserin aut Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA. Whole genome amplification (dpeaa)DE-He213 Multiple displacement amplification (dpeaa)DE-He213 Metagenomics (dpeaa)DE-He213 Droplet microfluidics (dpeaa)DE-He213 Amplification bias (dpeaa)DE-He213 Homa, Felix verfasserin aut Andersson-Svahn, Helene verfasserin aut Ettema, Thijs J. G. verfasserin aut Joensson, Haakan N. verfasserin aut Enthalten in Microbiome London : Biomed Central, 2013 4(2016), 1 vom: 06. Okt. (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:4 year:2016 number:1 day:06 month:10 https://dx.doi.org/10.1186/s40168-016-0197-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2016 1 06 10
language	English
source	Enthalten in Microbiome 4(2016), 1 vom: 06. Okt. volume:4 year:2016 number:1 day:06 month:10
sourceStr	Enthalten in Microbiome 4(2016), 1 vom: 06. Okt. volume:4 year:2016 number:1 day:06 month:10
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Whole genome amplification Multiple displacement amplification Metagenomics Droplet microfluidics Amplification bias
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container_title	Microbiome
authorswithroles_txt_mv	Hammond, Maria @@aut@@ Homa, Felix @@aut@@ Andersson-Svahn, Helene @@aut@@ Ettema, Thijs J. G. @@aut@@ Joensson, Haakan N. @@aut@@
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author	Hammond, Maria
spellingShingle	Hammond, Maria ddc 570 misc Whole genome amplification misc Multiple displacement amplification misc Metagenomics misc Droplet microfluidics misc Amplification bias Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
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topic_title	570 ASE Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis Whole genome amplification (dpeaa)DE-He213 Multiple displacement amplification (dpeaa)DE-He213 Metagenomics (dpeaa)DE-He213 Droplet microfluidics (dpeaa)DE-He213 Amplification bias (dpeaa)DE-He213
topic	ddc 570 misc Whole genome amplification misc Multiple displacement amplification misc Metagenomics misc Droplet microfluidics misc Amplification bias
topic_unstemmed	ddc 570 misc Whole genome amplification misc Multiple displacement amplification misc Metagenomics misc Droplet microfluidics misc Amplification bias
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title	Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
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title_full	Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
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author_browse	Hammond, Maria Homa, Felix Andersson-Svahn, Helene Ettema, Thijs J. G. Joensson, Haakan N.
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title_sort	picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
title_auth	Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
abstract	Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.
abstractGer	Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.
abstract_unstemmed	Background Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.
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title_short	Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
url	https://dx.doi.org/10.1186/s40168-016-0197-7
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author2	Homa, Felix Andersson-Svahn, Helene Ettema, Thijs J. G. Joensson, Haakan N.
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up_date	2024-07-03T17:26:02.236Z
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Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis

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