A high-throughput pipeline for DNA/RNA/small RNA purification from tissue samples for sequencing

被引：1

作者：

Xu, Jing ^{[1
]}

Pandoh, Pawan K. ^{[1
]}

Corbett, Richard D. ^{[1
]}

Smailus, Duane ^{[1
]}

Bowlby, Reanne ^{[1
]}

Brooks, Denise ^{[1
]}

McDonald, Helen ^{[1
]}

Haile, Simon ^{[1
]}

Chahal, Sundeep ^{[1
]}

Bilobram, Steve ^{[1
]}

Mungall, Karen L. ^{[1
]}

Mungall, Andrew J. ^{[1
]}

Coope, Robin ^{[1
]}

Moore, Richard A. ^{[1
]}

Zhao, Yongjun ^{[1
]}

Jones, Steven J. M. ^{[1
]}

Marra, Marco A. ^{[1
,2
]}

机构：

[1] Canadas Michael Smith Genome Sci Ctr BC Canc, 570 W 7th Ave, Vancouver, BC, Canada

[2] Univ British Columbia, Dept Med Genet, 2329 West Mall, Vancouver, BC, Canada

来源：

BIOTECHNIQUES | 2023年 / 75卷 / 02期

基金：

加拿大健康研究院; 加拿大自然科学与工程研究理事会;

关键词：

genomics; miRNA; nucleic acid purification; purification; RNA; RNA-Seq; sequencing;

D O I：

10.2144/btn-2023-0011

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

High-throughput total nucleic acid (TNA) purification methods based on solid-phase reversible immobilization (SPRI) beads produce TNA suitable for both genomic and transcriptomic applications. Even so, small RNA species, including miRNA, bind weakly to SPRI beads under standard TNA purification conditions, necessitating a separate workflow using column-based methods that are difficult to automate. Here, an SPRI-based high-throughput TNA purification protocol that recovers DNA, RNA and small RNA, called GSC-modified RLT+ Aline bead-based protocol (GRAB-ALL), which incorporates modifications to enhance small RNA recovery is presented. GRAB-ALL was benchmarked against existing nucleic acid purification workflows and GRAB-ALL efficiently purifies TNA, including small RNA, for next-generation sequencing applications in a plate-based format suitable for automated high-throughput sample preparation.

引用

页码：47 / 55

页数：9

共 25 条

[1] A lab-on-a-chip for rapid miRNA extraction [J].

Behrmann, Ole ;

Hugle, Matthias ;

Bronsert, Peter ;

Herde, Bettina ;

Heni, Julian ;

Schramm, Marina ;

Huefert, Frank T. ;

Urban, Gerald A. ;

Dame, Gregory .

PLOS ONE, 2019, 14 (12)

[2]

Boinovic K., 2019, SCI REP-UK, V9, P1

[3] The impact of child maltreatment on non-suicidal self-injury: data from a representative sample of the general population [J].

Brown, Rebecca C. ;

Heines, Stefanie ;

Witt, Andreas ;

Braehler, Elmar ;

Fegert, Joerg M. ;

Harsch, Daniela ;

Plener, Paul L. .

BMC PSYCHIATRY, 2018, 18

[4] JAGuaR: Junction Alignments to Genome for RNA-Seq Reads [J].

Butterfield, Yaron S. ;

Kreitzman, Maayan ;

Thiessen, Nina ;

Corbett, Richard D. ;

Li, Yisu ;

Pang, Johnson ;

Ma, Yussanne P. ;

Jones, Steven J. M. ;

Birol, Inanc .

PLOS ONE, 2014, 9 (07)

[5] Large-scale profiling of microRNAs for The Cancer Genome Atlas [J].

Chu, Andy ;

Robertson, Gordon ;

Brooks, Denise ;

Mungall, Andrew J. ;

Birol, Inanc ;

Coope, Robin ;

Ma, Yussanne ;

Jones, Steven ;

Marra, Marco A. .

NUCLEIC ACIDS RESEARCH, 2016, 44 (01) :e3

[6] BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters [J].

Chu, Justin ;

Sadeghi, Sara ;

Raymond, Anthony ;

Jackman, Shaun D. ;

Nip, Ka Ming ;

Mar, Richard ;

Mohamadi, Hamid ;

Butterfield, Yaron S. ;

Robertson, A. Gordon ;

Birol, Inanc .

BIOINFORMATICS, 2014, 30 (23) :3402-3404

[7] Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways [J].

Chun, Hye-Jung E. ;

Lim, Emilia L. ;

Heravi-Moussavi, Alireza ;

Saberi, Saeed ;

Mungall, Karen L. ;

Bilenky, Mikhail ;

Carles, Annaick ;

Tse, Kane ;

Shlafman, Inna ;

Zhu, Kelsey ;

Qian, Jenny Q. ;

Palmquist, Diana L. ;

He, An ;

Long, William ;

Goya, Rodrigo ;

Ng, Michelle ;

LeBlanc, Veronique G. ;

Pleasance, Erin ;

Thiessen, Nina ;

Wong, Tina ;

Chuah, Eric ;

Zhao, Yong-Jun ;

Schein, Jacquie E. ;

Gerhard, Daniela S. ;

Taylor, Michael D. ;

Mungall, Andrew J. ;

Moore, Richard A. ;

Ma, Yussanne ;

Jones, Steven J. M. ;

Perlman, Elizabeth J. ;

Hirst, Martin ;

Marra, Marco A. .

CANCER CELL, 2016, 29 (03) :394-406

[8] Statistical power analyses using G*Power 3.1: Tests for correlation and regression analyses [J].

Faul, Franz ;

Erdfelder, Edgar ;

Buchner, Axel ;

Lang, Albert-Georg .

BEHAVIOR RESEARCH METHODS, 2009, 41 (04) :1149-1160

[9] Complex heatmaps reveal patterns and correlations in multidimensional genomic data [J].

Gu, Zuguang ;

Eils, Roland ;

Schlesner, Matthias .

BIOINFORMATICS, 2016, 32 (18) :2847-2849

[10] Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis [J].

Haile, Simon ;

Pandoh, Pawan ;

McDonald, Helen ;

Corbett, Richard D. ;

Tsao, Philip ;

Kirk, Heather ;

MacLeod, Tina ;

Jones, Martin ;

Bilobram, Steve ;

Brooks, Denise ;

Smailus, Duane ;

Steidl, Christian ;

Scott, David W. ;

Bala, Miruna ;

Hirst, Martin ;

Miller, Diane ;

Moore, Richard A. ;

Mungall, Andrew J. ;

Coope, Robin J. ;

Ma, Yussanne ;

Zhao, Yongjun ;

Holt, Rob A. ;

Jones, Steven J. ;

Marra, Marco A. .

PLOS ONE, 2017, 12 (06)

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