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User guides and protocols

DNA & RNA

Reduction for oligonucleotides with thiol modifications protocol (610 KB)

Reduction for oligonucleotides with thiol modifications protocol (610 KB)

Resuspension of duplexed oligonucleotides (223 KB)

Resuspension of duplexed oligonucleotides (223 KB)

Annealing oligonucleotides (194 KB)

Annealing oligonucleotides (194 KB)

User-submitted methods

Cloning high-quality CRISPR libraries with oPools Oligo Pools Demonstrated Protocol (396 KB)

qPCR & PCR

PrimeTime Influenza Kit Demonstrated Protocol (205 KB)

PrimeTime Influenza Kit Demonstrated Protocol (205 KB)

Avian Influenza Type A H5 Primers and Probe Set Protocol Sheet (181 KB)

Avian Influenza Type A H5 Primers and Probe Set Protocol Sheet (181 KB)

PrimeTime One-Step 4X Broad-Range Master Mix Protocol (522 KB)

PrimeTime One-Step 4X Broad-Range Master Mix Protocol (522 KB)

PrimeTime One-Step RT-qPCR Master Mix protocol (391 KB)

PrimeTime One-Step RT-qPCR Master Mix protocol (391 KB)

rhAmp SNP Genotyping (472 KB)

rhAmp SNP Genotyping (472 KB)

RNase H2–Dependent PCR (rhPCR) protocol (628 KB)

RNase H2–Dependent PCR (rhPCR) protocol (628 KB)

qPCR Dye calibration on AB systems protocol (609 KB)

qPCR Dye calibration on AB systems protocol (609 KB)

PrimeTime qPCR Assay Plate resuspension protocol (183 KB)

PrimeTime qPCR Assay Plate resuspension protocol (183 KB)

PrimeTime Gene Expression Master Mix (278 KB)

PrimeTime Gene Expression Master Mix (278 KB)

PrimeTime Primer Plate Resuspension Protocol (184 KB)

PrimeTime Primer Plate Resuspension Protocol (184 KB)

PrimeTime qPCR Probe Assay Resuspension Protocol (223 KB)

PrimeTime qPCR Probe Assay Resuspension Protocol (223 KB)

PrimeTime qPCR Primers Resuspension Protocol (225 KB)

PrimeTime qPCR Primers Resuspension Protocol (225 KB)

CRISPR genome editing

Cas9

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Alt-R HDR Donor Oligos in induced pluripotent stem cells (iPSCs) (1.1 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Alt-R HDR Donor Oligos in induced pluripotent stem cells (iPSCs) (1.1 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and HDR Donor Oligos in primary T Cells (951 KB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and HDR Donor Oligos in primary T Cells (951 KB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Alt-R HDR Donor Blocks (1.1 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Alt-R HDR Donor Blocks (1.1 MB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 System and HDR Donor Oligos (878 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 System and HDR Donor Oligos (878 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Neon] (839 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Neon] (839 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Nucleofector] (879 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Nucleofector] (879 KB)

Alt-R CRISPR-Cas9 System: Cationic lipid delivery of CRISPR ribonucleoprotein complexes into mammalian cells (1.1 MB)

Alt-R CRISPR-Cas9 System: Cationic lipid delivery of CRISPR ribonucleoprotein complexes into mammalian cells (1.1 MB)

Alt-R CRISPR-Cas9_Delivery of ribonucleoprotein complexes into HEK-293 cells using the Lonza Nucleofector System (968 KB)

Alt-R CRISPR-Cas9_Delivery of ribonucleoprotein complexes into HEK-293 cells using the Lonza Nucleofector System (968 KB)

Alt-R CRISPR-Cas9 system—RNP electroporation, Neon Transfection system (508 KB)

Alt-R CRISPR-Cas9 system—RNP electroporation, Neon Transfection system (508 KB)

Alt-R CRISPR-Cas9 system—RNP electroporation, Gene Pulser Xcell system (655 KB)

Alt-R CRISPR-Cas9 system—RNP electroporation, Gene Pulser Xcell system (655 KB)

Alt-R CRISPR-Cas9 system—in vitro cleavage of target DNA with RNP complex (408 KB)

Alt-R CRISPR-Cas9 system—in vitro cleavage of target DNA with RNP complex (408 KB)

Alt-R Genome Editing Detection Kit (939 KB)

Alt-R Genome Editing Detection Kit (939 KB)

Homology-directed repair (HDR)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Alt-R HDR Donor Oligos in induced pluripotent stem cells (iPSCs) (1.1 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Alt-R HDR Donor Oligos in induced pluripotent stem cells (iPSCs) (1.1 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and HDR Donor Oligos in primary T Cells (951 KB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and HDR Donor Oligos in primary T Cells (951 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 System and HDR Donor Oligos (878 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 System and HDR Donor Oligos (878 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Neon] (839 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Neon] (839 KB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Megamer ssDNA Fragments (1.3 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and Megamer ssDNA Fragments (1.3 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and HDR Donor Oligos (1.2 MB)

Homology-directed repair using the Alt-R CRISPR-Cas9 System and HDR Donor Oligos (1.2 MB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Nucleofector] (879 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 and Megamer ssDNA Fragments [Neon] (839 KB)

Quick reference protocol: HDR with Alt-R CRISPR-Cas9 System and HDR Donor Oligos (878 KB)

Legacy protocols/guides for Alt-R HDR Enhancer

Cas12a (Cpf1)

Alt-R CRISPR-Cas12a System - Delivery of ribonucleoprotein complexes into HEK-293 cells using the Amaxa Nucleofector System Protocol (845 KB)

Alt-R CRISPR-Cas12a System - Delivery of ribonucleoprotein complexes into HEK-293 cells using the Amaxa Nucleofector System Protocol (845 KB)

Alt-R CRISPR-Cas12a Cpf1 System: Delivery of ribonucleoprotein complexes into Jurkat T cells using the Neon Transfection System Protocol (672 KB)

Alt-R CRISPR-Cas12a Cpf1 System: Delivery of ribonucleoprotein complexes into Jurkat T cells using the Neon Transfection System Protocol (672 KB)

Mutation detection

Alt-R Genome Editing Detection Kit (939 KB)

Alt-R Genome Editing Detection Kit (939 KB)

Next generation sequencing

Library prep

xGen 2S DNA Library Prep Kits Protocol (470 KB)

xGen 2S DNA Library Prep Kits Protocol (470 KB)

xGen Stubby Adapter-UDI Primers for Element Quick Reference Guide (540 KB)

xGen Stubby Adapter-UDI Primers for Element Quick Reference Guide (540 KB)

xGen cfDNA and FFPE DNA Library preparation for sequencing using Ultima Genomics UG 100 Demonstrated Protocol (1.8 MB)

xGen cfDNA and FFPE DNA Library preparation for sequencing using Ultima Genomics UG 100 Demonstrated Protocol (1.8 MB)

High-throughput hybridization-capture enrichment of long genomic fragments Demonstrated Protocol (2.8 MB)

High-throughput hybridization-capture enrichment of long genomic fragments Demonstrated Protocol (2.8 MB)

xGen Sample Indexing Products for Ultima Genomics Quick Reference Guide (1.3 MB)

xGen Sample Indexing Products for Ultima Genomics Quick Reference Guide (1.3 MB)

xGen Stubby Adapter-UDI Primers for DNBSEQ (810 KB)

xGen Stubby Adapter-UDI Primers for DNBSEQ (810 KB)

Preparing NGS libraries using the xGen DNA Library Prep Kit EZ and MGIEasy UDB Primers Adapter Kit for sequencing with the DNBSEQ-G400 system (1017 KB)

Preparing NGS libraries using the xGen DNA Library Prep Kit EZ and MGIEasy UDB Primers Adapter Kit for sequencing with the DNBSEQ-G400 system (1017 KB)

xGen cfDNA & FFPE DNA Library Prep MC Kit and Adept Library Compatibility Kit Demonstrated Protocol (1.9 MB)

xGen cfDNA & FFPE DNA Library Prep MC Kit and Adept Library Compatibility Kit Demonstrated Protocol (1.9 MB)

xGen cfDNA and FFPE DNA Library Prep Kit for Singular Genomics G4 Sequencing Demostrated Protocol (1.5 MB)

xGen cfDNA and FFPE DNA Library Prep Kit for Singular Genomics G4 Sequencing Demostrated Protocol (1.5 MB)

xGen cfDNA and FFPE DNA Library Prep Kit Analysis Guidelines (1.2 MB)

xGen cfDNA and FFPE DNA Library Prep Kit Analysis Guidelines (1.2 MB)

xGen DNA Library Prep Kit EZ and Adept Library Compatibility Kit Demonstrated Protocol (1.4 MB)

xGen DNA Library Prep Kit EZ and Adept Library Compatibility Kit Demonstrated Protocol (1.4 MB)

xGen DNA Library Prep Kit EZ and Element Elevate Index and Adapter Kit Demonstrated Protocol (1009 KB)

xGen DNA Library Prep Kit EZ and Element Elevate Index and Adapter Kit Demonstrated Protocol (1009 KB)

xGen UDI Primer plates Quick Reference Guide (610 KB)

xGen UDI Primer plates Quick Reference Guide (610 KB)

Input DNA Quantification Assay Demonstrated Protocol (412 KB)

Input DNA Quantification Assay Demonstrated Protocol (412 KB)

Quick reference guide: xGen Stubby Adapter and Indexing Primers (610 KB)

Quick reference guide: xGen Stubby Adapter and Indexing Primers (610 KB)

xGen Adaptase Module Protocol (1 MB)

xGen Adaptase Module Protocol (1 MB)

xGen Broad-Range RNA Library Prep Kit Protocol (1.8 MB)

xGen Broad-Range RNA Library Prep Kit Protocol (1.8 MB)

xGen DNA Library Prep EZ Kit and xGen DNA Library Prep EZ UNI Kit Protocol (1.5 MB)

xGen DNA Library Prep EZ Kit and xGen DNA Library Prep EZ UNI Kit Protocol (1.5 MB)

xGen RNA Library Prep Kit Protocol (1.5 MB)

xGen RNA Library Prep Kit Protocol (1.5 MB)

xGen DNA Library Prep MC Kit and xGen DNA Library Prep MC UNI Kit Protocol (1.2 MB)

xGen DNA Library Prep MC Kit and xGen DNA Library Prep MC UNI Kit Protocol (1.2 MB)

xGen cfDNA and FFPE DNA Library Prep v2 MC Kit Protocol (1.9 MB)

xGen cfDNA and FFPE DNA Library Prep v2 MC Kit Protocol (1.9 MB)

xGen Normalase Module Protocol (1.6 MB)

xGen Normalase Module Protocol (1.6 MB)

xGen ssDNA and Low-Input DNA Library Prep Kit Protocol (1.1 MB)

xGen ssDNA and Low-Input DNA Library Prep Kit Protocol (1.1 MB)

xGen Methyl-Seq DNA Library Prep Kit Protocol (1.3 MB)

xGen Methyl-Seq DNA Library Prep Kit Protocol (1.3 MB)

xGen Deceleration Module Protocol (722 KB)

xGen Deceleration Module Protocol (722 KB)

Quick reference guide: xGen Stubby Adapter and UDI Primer Pairs (670 KB)

Quick reference guide: xGen Stubby Adapter and UDI Primer Pairs (670 KB)

xGen UDI-UMI Adapters quick reference guide (778 KB)

xGen UDI-UMI Adapters quick reference guide (778 KB)

Analysis guideline: Demultiplexing Illumina sequencing data with UMIs (893 KB)

Analysis guideline: Demultiplexing Illumina sequencing data with UMIs (893 KB)

Analysis guideline: xGen UDI-UMI Adapters-Processing sequence data with unique molecular identifiers (UMIs).pdf (798 KB)

Analysis guideline: xGen UDI-UMI Adapters-Processing sequence data with unique molecular identifiers (UMIs).pdf (798 KB)

Analysis guidelines—library prep

Analysis guideline: xGen Prism DNA Library Prep Kit (1.7 MB)

Analysis guideline: xGen UDI-UMI Adapters-Processing sequence data with unique molecular identifiers (UMIs).pdf (798 KB)

Analysis guideline: Demultiplexing Illumina sequencing data with UMIs (893 KB)

Legacy protocols—library prep

Quick reference protocol: xGen Prism DNA Library Prep Kit (1.2 MB)

Quick reference guide: xGen Stubby Adapter and UDI Primer Pairs (670 KB)

Hybridization capture

xGen Hyb and Wash Reagents v3 Kit protocol (582 KB)

xGen Hyb and Wash Reagents v3 Kit protocol (582 KB)

xGen Exome Hybridization and Trinity Run Setup Quick Guide (173 KB)

xGen Exome Hybridization and Trinity Run Setup Quick Guide (173 KB)

xGen Exome Sequencing Kit Trinity for Element Using a 1-Hour Hybridization Reaction Demonstrated Protocol (511 KB)

xGen Exome Sequencing Kit Trinity for Element Using a 1-Hour Hybridization Reaction Demonstrated Protocol (511 KB)

xGen DNA Library Prep EZ UNI Kit - Element Biosciences Compatibility Protocol (1.3 MB)

xGen DNA Library Prep EZ UNI Kit - Element Biosciences Compatibility Protocol (1.3 MB)

xGen Exome Sequencing Kit Trinity for Element AVITI System Protocol (1.5 MB)

xGen Exome Sequencing Kit Trinity for Element AVITI System Protocol (1.5 MB)

High-throughput hybridization-capture enrichment of long genomic fragments Demonstrated Protocol (2.8 MB)

High-throughput hybridization-capture enrichment of long genomic fragments Demonstrated Protocol (2.8 MB)

xGen Hyb Panel Design Tool User Guide (1.1 MB)

xGen Hyb Panel Design Tool User Guide (1.1 MB)

xGen hybridization capture of Illumina Nextera DNA libraries Protocol (2.9 MB)

xGen hybridization capture of Illumina Nextera DNA libraries Protocol (2.9 MB)

xGen Hybridization Capture of DNA Libraries Protocol (2.9 MB)

xGen Hybridization Capture of DNA Libraries Protocol (2.9 MB)

Automation of xGen Hybridization Capture on the Sciclone G3 NGS Workstation Protocol (1.4 MB)

Automation of xGen Hybridization Capture on the Sciclone G3 NGS Workstation Protocol (1.4 MB)

Analysis Guideline: Processing sequence data for copy number variations (CNVs) (1.4 MB)

Analysis Guideline: Processing sequence data for copy number variations (CNVs) (1.4 MB)

Legacy protocols—hybridization capture

Amplicon sequencing

xGen HIV Amplicon Panel Protocol Addendum (168 KB)

xGen HIV Amplicon Panel Protocol Addendum (168 KB)

xGen Respiratory Virus Amplicon Panel Protocol Addendum (156 KB)

xGen Respiratory Virus Amplicon Panel Protocol Addendum (156 KB)

xGen Amplicon Panels for viral genome sequencing Protocol (1.6 MB)

xGen Amplicon Panels for viral genome sequencing Protocol (1.6 MB)

Sequencing SARS-CoV-2 with the Midnight Amplicon Panel Demonstrated Protocol (1.1 MB)

Sequencing SARS-CoV-2 with the Midnight Amplicon Panel Demonstrated Protocol (1.1 MB)

xGen DNA Library Prep: Sequencing SARS-CoV-2 with the ARTIC nCoV-2019 Amplicon Panel Demonstrated Protocol (1 MB)

xGen DNA Library Prep: Sequencing SARS-CoV-2 with the ARTIC nCoV-2019 Amplicon Panel Demonstrated Protocol (1 MB)

xGen 16S Amplicon Panel v2 and xGen ITS1 Amplicon Panel Protocol (1.2 MB)

xGen 16S Amplicon Panel v2 and xGen ITS1 Amplicon Panel Protocol (1.2 MB)

xGen Amplicon Panels for Oncology Research, Inherited Disease Research, and Sample Tracking Protocol (1.2 MB)

xGen Amplicon Panels for Oncology Research, Inherited Disease Research, and Sample Tracking Protocol (1.2 MB)

xGen HS EGFR Pathway Amplicon Panel Protocol (1.1 MB)

xGen HS EGFR Pathway Amplicon Panel Protocol (1.1 MB)

Legacy protocols—amplicon sequencing

Legacy data analysis guidelines—amplicon sequencing

Legacy sample data—amplicon sequencing

Genotyping sample data—rhAmpSeq analysis (40.5 MB)

Genes & gene fragments

Seamless Cloning Method (818 KB)

Seamless Cloning Method (818 KB)

Blunt-end cloning method protocol (807 KB)

Blunt-end cloning method protocol (807 KB)

TA cloning method protocol (899 KB)

TA cloning method protocol (899 KB)

User-submitted methods

Cloning high-quality CRISPR libraries with oPools Oligo Pools Demonstrated Protocol (396 KB)

Cloning high-quality CRISPR libraries with oPools Oligo Pools Demonstrated Protocol (396 KB)

Functional genomics

RNA knockdown using gapmer Antisense Oligonucleotides (ASOs) Demonstrated Protocol (978 KB)

RNA knockdown using gapmer Antisense Oligonucleotides (ASOs) Demonstrated Protocol (978 KB)

IDT miRNA Inhibitors resuspension (240 KB)

IDT miRNA Inhibitors resuspension (240 KB)

TriFECTa RNAi Kit User Guide (1.3 MB)

TriFECTa RNAi Kit User Guide (1.3 MB)

Resuspension of duplexed oligonucleotides (223 KB)

Resuspension of duplexed oligonucleotides (223 KB)

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