{"id":58,"date":"2019-06-24T13:44:12","date_gmt":"2019-06-24T13:44:12","guid":{"rendered":"https:\/\/cugbf.scienceweb.wpengine.com\/?page_id=58"},"modified":"2025-03-31T19:25:50","modified_gmt":"2025-03-31T19:25:50","slug":"genomics-services","status":"publish","type":"page","link":"https:\/\/scienceweb.clemson.edu\/cugbf\/genomics-services\/","title":{"rendered":"Genomics Services"},"content":{"rendered":"

[et_pb_section fb_built=”1″ admin_label=”Center Aligned Text ” _builder_version=”4.16″ background_color=”#f8fbfe” use_background_color_gradient=”on” background_color_gradient_direction=”135deg” background_color_gradient_stops=”#f66733 0%|#522d80 100%” background_color_gradient_start=”#f66733″ background_color_gradient_end=”#522d80″ background_image=”https:\/\/cugbf.scienceweb.wpengine.com\/wp-content\/uploads\/sites\/2\/2019\/06\/geometric-bg-overlay-01.jpg” background_blend=”overlay” custom_padding=”2.3%|0px|1.8%|0px||” animation_style=”zoom” animation_direction=”bottom” animation_intensity_zoom=”8%” animation_starting_opacity=”100%” global_colors_info=”{}”][et_pb_row _builder_version=”4.16″ global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.16″ text_font=”Nunito Sans||||||||” text_text_color=”#ffffff” text_font_size=”18px” text_line_height=”1.8em” header_font=”Nunito Sans|700|||||||” header_font_size=”56px” header_line_height=”1.3em” header_2_font=”||||||||” text_orientation=”center” background_layout=”dark” max_width=”700px” module_alignment=”center” global_colors_info=”{}”]<\/p>\n

Genomics Services<\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”Features CTA Section” _builder_version=”4.16″ custom_margin=”||1px|||” custom_padding=”40px|0px|5px|0px||” saved_tabs=”all” global_colors_info=”{}”][et_pb_row admin_label=”Left Sided Image” _builder_version=”4.16″ custom_padding=”60px|0px|94px|0px||” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.16″ text_font=”Nunito Sans|600|||||||” text_text_color=”#522d80″ text_font_size=”22px” text_line_height=”1.8em” header_font=”||||||||” header_text_align=”left” header_2_font=”Nunito Sans|700|||||||” header_2_text_color=”#535b7c” header_2_font_size=”35px” header_2_line_height=”1.3em” max_width=”700px” module_alignment=”center” global_colors_info=”{}”]<\/p>\n

The suite of short-read Illumina sequencers available at Clemson University allows us to harness the applications of Illumina\u2019s MiSeq, NextSeq 2000 and NovaSeq X to suit your sequencing needs. Our relationship with external genomic facilities enables us to facilitate long-read sequencing using PacBio technology.<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”Features” _builder_version=”4.16″ background_color=”#f8fbfe” custom_padding=”0px|0px|6px|0px||” global_colors_info=”{}”][et_pb_row admin_label=”Tittle” _builder_version=”4.16″ custom_padding=”80px|||||” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.16″ text_font=”Nunito Sans||||||||” text_text_color=”#959baf” text_font_size=”18px” text_line_height=”1.8em” header_font=”||||||||” header_text_align=”center” header_text_color=”#535b7c” header_2_font=”Nunito Sans|700|||||||” header_2_text_color=”#535b7c” header_2_font_size=”35px” header_2_line_height=”1.3em” text_orientation=”center” max_width=”700px” module_alignment=”center” global_colors_info=”{}”]<\/p>\n

Illumina sequencers <\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,1_3,1_3″ _builder_version=”4.16″ custom_padding=”||90px|||” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_blurb title=”MiSeq” image=”https:\/\/scienceweb.clemson.edu\/cugbf\/wp-content\/uploads\/sites\/2\/2019\/08\/system-banner-miseq.png” _builder_version=”4.20.2″ header_level=”h3″ header_font=”|700|||||||” hover_enabled=”0″ global_colors_info=”{}” sticky_enabled=”0″]<\/p>\n

MiSeq applications include targeted gene, small genome, amplicon, and 16S sequencing. As an available sequencing platform on Clemson\u2019s main campus, we can facilitate experimental design and use of the Illumina MiSeq bench-top sequencer for your microbial studies.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_blurb title=”NextSeq 2000″ image=”https:\/\/scienceweb.clemson.edu\/cugbf\/wp-content\/uploads\/sites\/2\/2025\/03\/nextseq-2000-150×150.png” _builder_version=”4.27.4″ header_level=”h3″ header_font=”|700|||||||” hover_enabled=”0″ global_colors_info=”{}” sticky_enabled=”0″ alt=”nextseq 2000″ title_text=”nextseq 2000″]<\/p>\n

NextSeq 2000 applications include gene expression profiling (RNAseq), exome sequencing, and whole-genome sequencing. At the heart of our facility, the NextSeq 2000 allows for high-throughput sequencing with a tunable turnaround time and data output. The NextSeq can be used for QC of libraries included in a large-scale project before sequencing on the NovaSeq X.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_blurb title=”NovaSeq X” image=”https:\/\/scienceweb.clemson.edu\/cugbf\/wp-content\/uploads\/sites\/2\/2025\/03\/novaseq-x-200×300.png” _builder_version=”4.27.4″ header_level=”h3″ header_font=”|700|||||||” hover_enabled=”0″ global_colors_info=”{}” alt=”novaseq x” title_text=”novaseq x” sticky_enabled=”0″]<\/p>\n

Through our relationship with the College of Science\u2019s Center for Human Genetics in Greenwood, SC, we can leverage the power and cost effectiveness of Illumina\u2019s NovaSeq X to suit the needs of large-scale sequencing projects. Key applications of the NovaSeq X include whole-genome, whole-exome, and whole-transcriptome sequencing.<\/p>\n

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To determine your desired sequencing coverage, use one of the sequencing coverage calculators from Illumina<\/a><\/span><\/strong> and New England Biolabs<\/a><\/span><\/strong>. For further assistance, contact us<\/a><\/span><\/strong>.<\/span><\/p>\n

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For your long-read sequencing needs, Pacific Biosciences sequencing can be completed through our relationship with external genomics facilities. Please contact us<\/a><\/span><\/strong> so we can facilitate your long-read sequencing projects.<\/span><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.16″ custom_padding=”||99px|||” global_colors_info=”{}”][et_pb_column type=”1_2″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_image src=”https:\/\/scienceweb.clemson.edu\/cugbf\/wp-content\/uploads\/sites\/2\/2023\/09\/IMG_4025-scaled-e1694437162267.jpg” alt=”IMG 4025″ title_text=”Agilent TapeStation 4200″ _builder_version=”4.20.2″ global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.20.2″ text_font=”||||||||” text_text_color=”#86898c” width=”100%” custom_padding=”|0px||||” global_colors_info=”{}”]<\/p>\n

Agilent TapeStation 4200<\/strong><\/h2>\n

The Agilent TapeStation is an automated electrophoresis system that has both DNA and RNA applications. Quantify and size DNA samples. Additionally, RNA samples can be checked for quality by generating an RNA Integrity Number (RIN). The TapeStation uses as little as 1mL of sample for quality control analysis. The fully automated system can handle 1-96 samples at a time making it perfect for both small and large sample sets. The TapeStaiton can be utilized for NGS library preparation and NGS workflows. \u00a0<\/span><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.16″ custom_padding=”100px||99px|||” global_colors_info=”{}”][et_pb_column type=”1_2″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.20.2″ text_font=”||||||||” text_text_color=”#86898c” global_colors_info=”{}”]<\/p>\n

Invitrogen Qubit and Qubit Flex Fluorometer<\/strong><\/h2>\n

The Qubit benchtop fluorometer is designed to accurately measure DNA, RNA, and protein quantity with as little as 1mL of sample. The Qubit also easily measures RNA integrity and quality. The Qubit Flex shares common features with the Qubit but allows for the analysis of 8 samples at a time and is perfect for the quantification of a large numbers of samples. \u00a0The Qubit and Qubit Flex fluorometers can be utilized for DNA library QC in NGS workflows.\u00a0<\/span><\/p>\n

[\/et_pb_text][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_image src=”https:\/\/scienceweb.clemson.edu\/cugbf\/wp-content\/uploads\/sites\/2\/2023\/09\/IMG_4024-scaled-e1694437241221.jpg” alt=”IMG 4024″ title_text=”Invitrogen Qubit and Qubit Flex Fluorometer” _builder_version=”4.20.2″ global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.20.2″ _module_preset=”default” min_height=”23px” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.20.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.20.2″ _module_preset=”default” global_colors_info=”{}”]<\/p>\n

Services Offered<\/strong><\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.16″ min_height=”957.5px” custom_padding=”0px|||||” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_accordion _builder_version=”4.20.2″ toggle_level=”h3″ global_colors_info=”{}”][et_pb_accordion_item title=”RNA Isolation” open=”on” _builder_version=”4.16″ global_colors_info=”{}”]<\/p>\n

Obtaining high-quality RNA is a crucial step in performing molecular techniques such as RT-qPCR, transcriptome analysis using NGS, digital PCR, and cDNA library construction. The RNA isolation protocol can be tailored to specific sample types and optimized for varying storage conditions.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”DNA Isolation” _builder_version=”4.16″ global_colors_info=”{}” open=”off”]<\/p>\n

Downstream applications of DNA isolation may include DNA sequencing, DNA bioanalyzer analysis and PCR. The isolation protocol may vary with sample types.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”HMW DNA Isolation” _builder_version=”4.16″ global_colors_info=”{}” open=”off”]<\/p>\n

Long read sequencing protocols depends on high-quality DNA samples. We aim to isolate HMW-DNA samples with mean fragment lengths of 50 kb or higher. The isolation protocol may vary with sample types.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”Chromatin Immunoprecipitation” _builder_version=”4.16″ global_colors_info=”{}” open=”off”]<\/p>\n

Commonly used to test whether a protein of interest associates with a target DNA site in vivo. ChIP followed by next-generation sequencing enables the mapping of binding loci throughout the genome with a high resolution. When combined with the transcriptomics data, ChIP-seq can be used to determine the regulon of a regulatory protein. Additionally, ChIP-seq can provide clues about potential co-regulatory proteins.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”Agilent 2100 Bioanalyzer ” _builder_version=”4.20.2″ global_colors_info=”{}” open=”off”]<\/p>\n

The 2100 Bioanalyzer system features automated electrophoresis for nucleic acid quality control. Applications include DNA size and quantity, RNA quality check with RIN and protein analysis. The 2100 Bioanalyzer is utilized for DNA library QC in NGS workflows.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”NGS Library Preparation” _builder_version=”4.16″ global_colors_info=”{}” open=”off”]<\/p>\n

The NGS library preparation utilizes Illumina or other supported kits based on quantity and physical characteristics of RNA or DNA source material as well as the desired application. Library preparation involves generating a collection of DNA fragments for sequencing.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”KAPA Library Quantification” _builder_version=”4.16″ global_colors_info=”{}” open=”off”]<\/p>\n

KAPA library quantification is qPCR-based quantification of NGS libraries prior to pooling and used after pooling. This method enables accurate pooling of libraries for multiplexed sequencing and can also be performed after pooling as a confirmatory step before sequencing. KAPA library quantification is recommended in conjunction with Qubit and Bioanalyzer analysis.<\/p>\n

[\/et_pb_accordion_item][et_pb_accordion_item title=”Blue Pippin Prep ” _builder_version=”4.16″ global_colors_info=”{}” open=”off”]<\/p>\n

The Blue Pippin is utilized for DNA size selection (up to 50kb) for NGS. Desired target sizes or ranges of sizes are entered in software and fractions are collected in buffer. Up to 5 samples\/gel cassette may be run, with no possibility of cross contamination.<\/p>\n

[\/et_pb_accordion_item][\/et_pb_accordion][et_pb_button button_url=”\/cugbf\/bioinformatics-services\/” button_text=”Bioinformatics Services” button_alignment=”right” _builder_version=”4.16″ custom_button=”on” button_font=”||||||||” button_icon=”9||divi||400″ button_icon_color=”#522d80″ button_on_hover=”off” global_colors_info=”{}”][\/et_pb_button][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”Testimonial” _builder_version=”4.16″ custom_padding=”5px|0px|100px|0px||” global_colors_info=”{}”][et_pb_row admin_label=”Testimonial Row” _builder_version=”4.16″ custom_margin=”99px|auto||auto||” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_blurb title=”\u201cA well-functioning Genomics & Bioinformatics Facility is essential to successful research at Clemson.\u201d ” admin_label=”Testimonial” _builder_version=”4.16″ header_level=”h2″ header_font=”Nunito Sans|700|||||||” header_text_color=”#535b7c” header_line_height=”1.4em” body_font=”Nunito Sans|600|||||||” body_text_color=”#959baf” body_font_size=”16px” background_image=”https:\/\/cugbf.scienceweb.wpengine.com\/wp-content\/uploads\/sites\/2\/2019\/06\/quote-bg.png” background_size=”initial” text_orientation=”center” global_colors_info=”{}”]<\/p>\n

\u2014 Dr. David Freedman<\/strong><\/span>
Department of Environmental Engineering and Earth Sciences<\/strong><\/span>
Clemson University<\/strong><\/span><\/p>\n

[\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”Get Started CTA” _builder_version=”4.16″ background_color=”#202332″ custom_padding=”0px|0px|100px|0px” box_shadow_style=”preset3″ box_shadow_vertical=”160px” box_shadow_blur=”0px” box_shadow_spread=”-80px” box_shadow_color=”#ffffff” box_shadow_position=”inner” saved_tabs=”all” global_colors_info=”{}”][et_pb_row column_structure=”2_3,1_3″ admin_label=”CTA Row” _builder_version=”4.16″ use_background_color_gradient=”on” background_color_gradient_direction=”243deg” background_color_gradient_stops=”#522d80 0%|#f66733 100%” background_color_gradient_start=”#522d80″ background_color_gradient_end=”#f66733″ custom_padding=”32px|40px||40px” border_radii=”on|4px|4px|4px|4px” saved_tabs=”all” global_colors_info=”{}”][et_pb_column type=”2_3″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.16″ text_font=”Nunito Sans||||||||” text_text_color=”#ffffff” text_font_size=”15px” header_font=”Nunito Sans|700|||||||” header_text_align=”left” header_text_color=”#ffffff” header_font_size=”35px” header_line_height=”1.4em” header_2_font=”Nunito Sans|700|||||||” header_2_text_align=”left” header_2_text_color=”#ffffff” header_2_font_size=”35px” header_2_line_height=”1.4em” header_3_font=”||||||||” header_4_font=”||||||||” header_5_font=”||||||||” header_6_font=”||||||||” custom_margin=”||| ” global_colors_info=”{}”]<\/p>\n

Ready To Get Started?<\/h2>\n

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Genomics ServicesThe suite of short-read Illumina sequencers available at Clemson University allows us to harness the applications of Illumina\u2019s MiSeq, NextSeq 2000 and NovaSeq X to suit your sequencing needs. Our relationship with external genomic facilities enables us to facilitate long-read sequencing using PacBio technology.Illumina sequencers MiSeq applications include targeted gene, small genome, amplicon, and […]<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-58","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/pages\/58","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/comments?post=58"}],"version-history":[{"count":0,"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/pages\/58\/revisions"}],"wp:attachment":[{"href":"https:\/\/scienceweb.clemson.edu\/cugbf\/wp-json\/wp\/v2\/media?parent=58"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}