OSTR | Office of Science and Technology Resources

Sequencing Facility

Overview

CCR Sequencing Facility

Mission:

The mission of the Center for Cancer Research Sequencing Facility (CCR-SF) is to utilize high-throughput sequencing technologies to enrich cancer research and ensure that the NCI community can leverage the leading-edge of Next-Generation Sequencing technology.

CCR Sequencing Facility: Overview

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at previously unthinkable speeds and a fraction of their former cost. At the Sequencing Facility, NCI researchers are provided access to the latest technologies, with consultation and Q&A services available throughout the design and execution of sequencing projects.

Our lab currently employs the following sequencing platforms:


NovaSeq 6000

Illumina (Short Read) Sequencing Technology

  • Illumina sequencing utilizes reversible terminator chemistry optimized to achieve high levels of cost-effectiveness and throughput
  • Millions of reads produced per sample lane at 50 bp to 300 bp read lengths
  • Support for the multiplexing of 96 bar-coded samples into a single lane
  • Available resources include  NovaSeq6000,  NextSeq2000 and MiSeq sequencer


PacBio RS

Long-Read Technologies: PacBio Sequel IIe Sequencing

  • Amplification-free sequencing via Single-Molecule Real-Time (SMRT) technology enables rapid identification of long nucleotide chains and DNA methylation. 
  • HiFi reads generated using Circular Consensus Sequencing mode (up to 25 kb read length) achieve > 99.9% accuracy.
  • Long and accurate reads are ideal for many applications such as de novo assemblies, identification of structural variants, full-length transcriptomes and long amplicons.
  • Average yields per SMRTcell are insert-size dependent but can reach 30 Gb of HiFi reads for WGS.
  • Project flexibility with production protocols that include large and small genome sequencing, whole and targeted transcriptome sequencing (Iso-Seq) for bulk and single cell sample, and amplicon sequencing, either single or multiplexed.

GridION

P2Solo

Long-Read Technologies: Oxford Nanopore Technologies (ONT)

  • ONT sequencing uses flow cells containing an array of tiny holes — nanopores — embedded in an electro-resistant membrane. When a molecule passes through a nanopore, the current is disrupted to produce a characteristic ‘squiggle’. The squiggle is then decoded using basecalling algorithms to determine the DNA or RNA sequence.
  • ONT can analyze native DNA or RNA in real-time and sequence any length of fragment to achieve short (20 bases) to ultra-long read lengths (> 1 million bases), with accuracies over 99%.
  • Amplification-free direct sequencing of individual DNA and RNA molecules precludes PCR bias and artifacts and allows base modification identification at single nucleotide resolution, including 5mC, 5hmC in DNA and m6A in RNA. Detection of further natural or synthetic epigenetic modifications are possible through training basecalling algorithms.de novo assemblies, identification of structural variants, full-length transcriptomes and long amplicons.
  • The Sequencing Facility offers several ONT devices with different throughput capacities: GridION (up to 50 GB per flow cell) and PromethION 2 Solo (up to 200 GB per flow cell).
  • Minimal machine turnaround time provides flexibility in experimental and run design, including whole and targeted genome sequencing, whole transcriptome sequencing for bulk and single cell samples and direct RNA sequencing.

Single Cell

Single Cell Technologies: 10X Genomics

  • 10X Genomics Chromium X system can partition hundreds of thousands of fresh, frozen, or fixed cells in a single run.
  • The system can easily handle a range of projects, from a pilot size study to the highest-throughput analysis.
  • Chromium X system is compatible with all 10X Genomics single cells assays and can capture molecular readouts of cell activity in multiple dimensions, including gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity.

Single Cell Technologies: Mission Bio

  • Mission Bio Tapestri platform can provide both genotype and phenotype data from the same cell.
  • The Tapestri Platform enables targeted single-cell DNA and protein analysis.
  • Tapestri Single-cell DNA panels allow researchers to focus on the mutations and regions of interest that are most relevant to their disease research.
  • The targeted single cell DNA panel can detect SNVs, CNVs and proteins simultaneously from the same cell.

Single Cell Technologies: Fluent BioSciences PIPseq

  • Instrument-free single-cell RNA-seq (3’ gene end counting)
  • Fast and scalable scRNA-seq technology, works as well as 10X assays. Cost effective.
  • Low multiplet rate
  • High quality transcript capture and complex cell population resolution
  • Application areas: Cancer, Immunology, neurosciences, infectious diseases

Bionano Saphyr

Optical Mapping Technologies: Bionano Genomics

  • Bionano’s non-sequencing-based genome mapping technology images and analyzes extremely long, high-molecular-weight DNA.
  • Facilitates identification of structural variants and creation of de novo genome assemblies.

Services

SF Services

To request services from the CCR Sequencing Facility
Submit a Sequencing Facility Request
Prior to filling out a NAS request, you are advised to consult with Dr. Maggie Cam and/or Mr. Bao Tran to discuss your project design and bioinformatics approach to data analysis:

Bao Tran
Director, Sequencing Facility
bao.tran@nih.gov
301-360-3460

Maggie Cam, Ph.D.
maggie.cam@nih.gov
301-443-2965

Please visit the Protocols and Resources page for more details about the sequencing chemistry and technology utilized by each platform. We encourage you to contact us so we can provide you with the most current information and help you plan your project to meet your sequencing needs.

Short reads with Illumina Sequencing:

Illumina sequencing enables a wide variety of applications, allowing researchers to ask virtually any question related to the genome, transcriptome, or epigenome of any organism.

  • ChIP-Seq
  • Cut and Run
  • ATAC-Seq*
  • RNA-Seq (mRNA, Total RNA and microRNA)
  • Whole Genome Sequencing
  • Whole Exome Sequencing – For further information please contact NCI-FredLMTSFExome@mail.nih.gov.
  • Methylated DNA sequencing (bisulfite)
  • Amplicon Sequencing
* ATAC seq is only provided as a pilot project for a maximum of 12 samples. After the pilot, or for more than 12 samples, we can transfer the protocol to you.

Long Read Sequencing Techonologies:

  • Whole Genome Sequencing: de novo assembly, haplotype resolution, structural variant detection, DNA epigenetic modification detection.
  • RNA Sequencing: Full-length transcript sequencing for whole-transcriptome or gene-specific targets. Full-length RNA sequencing can be performed on bulk or single cell samples. Direct RNA sequencing with Oxford Nanopore Sequencing.
  • Targeted Sequencing: Long amplicon sequencing, full-length viral sequencing, full-length vector sequencing, target enrichment, adaptive sampling and multiplexing strategies.
  • HLA Typing: Amplification of full gene for HLA class I and/or class II.
  • 16S sequencing: Amplification of full length 16S for bacterial communities.

Optical Mapping using Bionano Technology:

Imaging and analysis of extremely long, high-molecular-weight DNA facilitates identification of structural variants and creation of de novo genome assemblies

Single-cell Sequencing:

  • Single-cell transcriptomics: 10X Genomics single-cell gene expression (3’ or 5’ gene end counting) analysis
  • Single-cell immune repertoire analysis: 10X Genomics single-cell VDJ (TCR / BCR; human/mouse) solution with or without 5’ gene expression profiling
  • 10X Genomics Gene Expression with Cell Surface Protein Expression (CITE-Seq) and/or sample multiplexing with barcoded antibody labeling (Cell hashing)
  • Single-cell epigenomic analysis: 10x Genomics single-cell ATAC-Seq solution
  • Single-cell genomics: Targeted DNA panels and Mission Bio Tapestri platform
  • Single-cell targeted DNA and protein analysis: Targeted DNA panels, barcoded antibody labeling, and Mission Bio Tapestri platform
  • Single-cell fixed RNA profiling (mouse/human): whole transcriptome analysis of PFA-fixed human or mouse samples by using 10X Chromium Fixed RNA profiling solution
  • Single-cell Iso-Seq (full length RNA-seq): Targeted or Whole Transcriptome Full-Length scRNA-Seq on PacBio and Oxford Nanopore sequencing platforms
  • Instrument free single-cell transcriptomics: Fluent Biosciences PIPSeq single-cell gene Expression (3’ gene end counting) analysis

R&D Resources:

  • R&D group works closely with investigators to provide customized support for a variety of applications, utilizing the most recent state-of-the-art NGS sequencing technologies.
  • Testing and validation of new sequencing applications/products before offering them as production services.
  • Development of new sequencing applications/protocols to assist the NCI community.
  • Training the production team members and PI labs on the newest developed NGS sequencing technologies and new instruments.

Bioinformatics Support:

CCR-SF bioinformatics group provides coordinated joint consultation services for sequencing technology selection, project design, and data analysis for next generation sequencing projects. We support analysis for Whole Genome/Exome sequencing, ATAC-seq, ChIP-seq, RNA-seq, miRNA-seq and analysis for new data types from single cell sequencing, long-read sequencing and optical mapping. We work collaboratively with the CCR Collaborative Bioinformatics Resource (CCBR) and provide a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals.

Pricing

Illumina Library Construction

CCR/NIAID Price Non CCR Price**
Project Type Cost/Sample Cost/Sample
ChIP-Seq $88 + (Seq Cost) $132 + (Seq Cost)
gDNA-Seq $47 + (Seq Cost) $71 + (Seq Cost)
Nextera DNA Flex $61 + (Seq Cost) $91 + (Seq Cost)
Whole Genome Methyl-Seq $95+ (Seq Cost) $142 + (Seq Cost)
Total RNA-Seq $113 + (Seq Cost) $170 + (Seq Cost)
mRNA-Seq $110 + (Seq Cost) $165 + (Seq Cost)
miRNA-Seq $99 + (Seq Cost) $148 + (Seq Cost)
ATAC-Seq $101 + (Seq Cost) $152 + (Seq Cost)

Illumina Sequencing

*Due to lower consumable prices the 33% CCR subsidy is no longer available for NovaSeq runs.
NovaSeq 6000 CCR/NIAID Price Non CCR Price**
Run Type Cost/Sample Cost/Sample
SP 100 Cycle $2,261 $3,391
SP 200 Cycle $2,960 $4,440
SP 300 Cycle $3,229 $4,843
SP 500 Cycle $4,520 $6,780
S1 100 Cycle $4,143 $6,215
S1 200 Cycle $5,220 $7,829
S1 300 Cycle $5,650 $8,475
S2 100 Cycle $7,803 $11,704
S2 200 Cycle $9,686 $14,529
S2 300 Cycle $10,332 $15,498
S4 200 Cycle $13,910 $20,866
S4 300 Cycle $15,498 $23,247
XP 2-Lane Kit $321 $482
XP 4-Lane Kit $645 $967
NextSeq 2000 CCR/NIAID Price Non CCR Price**
Run Type Cost/Sample Cost/Sample
P2 100 Cycle $1,529 $2,293
P2 200 Cycle $2,874 $4,311
P2 300 Cycle $3,810 $5,716
P3 100 Cycle $3,489 $5,246
P3 200 Cycle $4,844 $7,265
P3 300 Cycle $6,458 $9,686
MiSeq CCR/NIAID Price Non CCR Price**
Run Type Cost/Sample Cost/Sample
1 x 50 Cycle (V2) $980 $1,469
1 x 300 Cycle (V2) $1,254 $1,881
1 x 500 Cycle (V2) $1,410 $2,115
1 x 150 Cycle (V3) $1,087 $1,630
1 x 600 Cycle (V3) $1,835 $2,753

Single Cell 10X Chromium Library Construction

CCR/NIAID Price Non CCR Price**
Project Type Cost/Sample Cost/Sample
10X Chromium single-cell RNA-seq (GEX, for 3′ or 5′) $1,668 + (Seq Cost) $2,502 + (Seq Cost)
10X Chromium single-cell VDJ Enrichment (TCR or BCR, for 5’ only) $105 + (10X Capture) + (Seq Cost) $157 + (10X Capture) + (Seq Cost)
10X Chromium single-cell Feature Barcode (for 3’ or 5’) $123 + (10X Capture) + (Seq Cost) $184 + (10X Capture) + (Seq Cost)
10X Chromium single-cell ATAC-seq $1,522 + (Seq Cost) $2,283 + (Seq Cost)
10X Chromium HT Single Cell RNA_Seq (GEX, for 3′ or 5′) $1,722 + (Seq Cost) $2,583 + (Seq Cost)
10X Chromium Fixed RNA_Seq $1,477 + (Sequencing Cost) $2,215 + (Sequencing Cost)

Single Cell Mission Bio Tapestri Library Construction Prices

*Custom DNA panel price is not included. Please communicate with Mission Bio
CCR/NIAID Price Non CCR Price**
Project Type Cost/Sample Cost/Sample
Tapestri Single Cell DNA* $2,231 + (Sequencing Cost) $3,347 + (Sequencing Cost)
Tapestri Single Cell DNA and Protein (multi-omics) $2,494 + (Sequencing Cost) $3,741 + (Sequencing Cost)
Tapestri Single -Cell Targeted DNA panels (AML, Myeloid, THP, CLL) + (Capture) $66 + (Capture) + (Sequencing Cost) $98 + (Capture) + (Sequencing Cost)

Pacbio Library Construction

CCR/NIAID Price Non CCR Price**
Project Type Cost/Sample Cost/Sample
Amplicon Multiplex $88 + (Seq Cost) $132 + (Seq Cost)
RNA-Iso-Seq $125 + (Seq Cost) $187 + (Seq Cost)
Whole Genome Sequencing $135 + (Seq Cost) $203 + (Seq Cost)
HLA Class I + II $186 + (Seq Cost) $279 + (Seq Cost)
Full Length 16S $7 + (Seq Cost) $11 + (Seq Cost)
Single cell MAS iso-seq $238 + (Seq Cost) $357 + (Seq Cost)
Single cell MAS iso-seq + Jumpcode depletion $487 + (Seq Cost) $731 + (Seq Cost)

Pacbio Sequencing

CCR/NIAID Price Non CCR Price**
Run Type Cost/Sample Cost/Sample
SMRT Cell $1,200 $1,800

Oxford Nanopore Library Construction

CCR/NIAID Price Non CCR Price**
Project Type Cost/Sample Cost/Sample
NanoPore WGS $138 + (Seq Cost) $207 + (Seq Cost)
NanoPore Direct RNA-Seq $132 + (Seq Cost) $198 + (Seq Cost)
NanoPore Iltra-Long $242 + (Seq Cost) $363 + (Seq Cost)

Oxford Nanopore Sequencing

CCR/NIAID Price Non CCR Price**
Run Type Cost/Sample Cost/Sample
ONT Flow Cell R9.4.1/R10.4.1 $900 $1,350

Bionano Genomics Optical Mapping Sample Prep

CCR/NIAID Price Non CCR Price**
Project Type Cost/Sample Cost/Sample
Bionano Sample Prep for Blood and Cell $195 + (Seq Cost) $293 + (Seq Cost)

Bionano Genomics Sequencing

CCR/NIAID Price Non CCR Price**
Run Type Cost/Sample Cost/Sample
1 Sample $1,100 $1,650
2 Samples $825 $1,238
Set of 3 Samples $549 $824

Protocols and Resources

SF Protocols and Resources

Here you will find all the forms necessary for submitting your sequencing proposal and samples to the laboratory. To aid in project planning, we have also provided handouts of the technical details of each sequencing platform as well as the sample preparation protocols used by our laboratory. Do you have additional questions about the Sequencing Facility? Check out our sequencing FAQs, containing the most common questions we receive!

Laboratory Forms and Information
Illumina PacBio

Protocols and Resources
Illumina PacBio

Bioinformatics Information

Specialized in NGS data analysis and quality control, CCR-SF bioinformatics team works closely with CCR researchers to provide support services such as sequencing technology consultation, experimental design, and data analysis and management. Please visit the Frequently Asked Questions for more information.

Bioinformatics Resources and FAQ

Publications

Publications

2019

Zhao Y*, Mehta M*, Walton A*, Talsania K*, Levin Y, Shetty J, Gillanders EM, Tran B, Carrick DM. Robustness of RNA sequencing on older formalin-fixedparaffin-embedded tissue from high-grade ovarian serous adenocarcinomas. PLoS  2019 May 6;14(5): e0216050.

Levin Y†, Talsania K†, Tran B, Shetty J*, Zhao Y*, Mehta M*. Optimization for sequencing and analysis of degraded FFPE-RNA samples. JoVE, In Press. († Co-first authors; * Co-corresponding authors)

Magen A, Nie J, Ciucci T, Tamoutounour S, Zhao Y, Mehta M, Tran B, McGavern DB, Hannenhalli S, Bosselut R. Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+T Cells. Cell Reports, 2019, 29(10):  3019-3032.e6

The Somatic Mutation Working Group of the SEQC-II consortium, Xiao W, Kusko R, Ren L, Fang F, Shen T, Talsania K, Kriga Y, Shetty J, Tran B, Zhao Y, et al. Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing.  Nat Biotechnol, 2019. Accepted

Ma L, Hernandez M, Zhao Y, Mehta M, Tran B, Kelly M, Rae Z, Hernandez J, Davis J, Martin S, Kleiner D, Hewitt S, Ylaya K, Wood B, Greten T, Wang X. Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer.  Cancer Cell. 2019 Oct 03.

Jiao X, Sui H, Lyons C, Tran B, Sherman BT, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 1 Strain McKrae. Microbiol Resour Announc. 2019 Sep 26;8(39).

Jiao X, Sui H, Lyons C, Tran B, Sherman BT, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 1 Strain MacIntyre. Microbiol Resour Announc. 2019 Sep 12;8(37).

Vacchio MS, Ciucci T, Gao Y, Watanabe M, Balmaceno-Criss M, McGinty MT, Huang A, Xiao Q, McConkey C, Zhao Y, Shetty J, Tran B, Pepper M, Vahedi G, Jenkins MK,  McGavern DB, Bosselut R. A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation. Immunity.  2019 Sep 17;51(3):465-478.e6. Epub 2019 Aug 15.

Talsania K, Mehta M, Raley C, Kriga Y, Gowda S, Grose C, Drew M, Roberts V, Tai Cheng K, Burkett S, Oeser S, Stephens R, Soppet D, Chen X, Kumar P, German O, Smirnova T, Hautman C, Shetty J, Tran B, Zhao Y, & Esposito D. Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies. Gene, 2019, 10 (2). pii: E79.

Ciucci T, Vacchio MS, Gao Y, Ardori FT, Candia J, Mehta M, Zhao Y, Tran B, Tessarollo L, McGavern D, & Bosselut R. Emergence and functional fitness of memory CD4+ T cells require the transcription factor Thpok. Immunity, 2019, 50(1): 91-105.e4.

2018

Zheng H, Pomyen Y, Hernandez MO, Li C, Livak F, Tang W, Dang H, Greten T, Zhao Y, Mehta M, Levin Y, Shetty J, Tran B, Budhu A, and Wang XW. Single cell analysis reveals cancer stem cell heterogeneities in hepatocellular carcinoma. Hepatology, 2018, 68(1): 127-140.

Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W,  Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407.

Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M:De Novo assembly and phasing of dikaryotic genomes from two isolates of puccinia coronata f. sp. avenae, the causal agent of oat crown rust. MBio, 9(1):2018.

Greer YE, Porat-Shliom N, Nagashima K, Stuelten C, Crooks D, Koparde VN, Gilbert SF, Islam C, Ubaldini A, Ji Y, Gattinoni L, Soheilian F, Wang X, Hafner M, Shetty J, Tran B, Jailwala P, Cam M, Lang M, Voeller D, Reinhold WC, Rajapakse V, Pommier Y, Weigert R, Linehan WM, Lipkowitz S. ONC201 kills breast cancer cells in vitro by targeting mitochondria. Oncotarget. 2018 Apr 6;9(26):18454-18479.

Cramer SD, Hixon JA, Andrews C, Porter RJ, Rodrigues GOL, Wu X, Back T, Czarra K, Michael H, Cam M, Chen J, Esposito D, Senkevitch E, Negi V, Aplan PD, Li W, Durum SK. Mutant IL-7Rα and mutant NRas are sufficient to induce murine T cell acute lymphoblastic leukemia. Leukemia. 2018 Aug;32(8):1795-1882.

2017

Shukla A, Zhu J, Kim SY, Hager G, Ruan Y and Hunter KW (2017) Identification of a core inherited metastatic susceptibility network by integrated epigenetic, genetic and chromosomal interaction analysis.  Manuscript in preparation

Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao Y, Shetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R. Control of Regulatory T Cell Differentiation by the Transcription Factors Thpok and LRF.   J Immunol. 2017 Sep 1;199(5): 1716-1728.

2016

Hodson DJ, Shaffer AL, Xiao W, Wright GW, Schmitz R, Phelan JD, Yang Y, Webster DE, Rui L, Kohlhammer H, Nakagawa M, Waldmann TA, Staudt LM.  Regulation of normal B cell differentiation and malignant B cell survival by OCT2.  Proc Natl Acad Sci 2016 113:E2039-E2046.

Thompson, Bethtrice; Varticovski, Lyuba; Baek, Songjoon; et al. Hager GL. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLOS ONE   Volume: 11   Issue: 2

Yang Y, Kelly P, Shaffer AL, Schmitz R, Liu X, Huang DW, Webster D, Young RM, Yoo H, Nakagawa M, Ceribelli M, Wright GW, Yang Y, Zhao H, Yu X, Xu W, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza L, Staudt LM.  Targeting non-proteolytic protein ubiquitination for the treatment of diffuse large B cell lymphoma.  Cancer Cell 2016 29:494-507.

Kuschal C, Botta E, Orioli D, Digiovanna JJ, Seneca S, Keymolen K, Tamura D, Heller E, Khan SG, Caligiuri G, Lanzafame M, Nardo T, Ricotti R, Peverali FA, Stephens R, Zhao Y, Lehmann AR, Baranello L, Levens D, Kraemer KH, Stefanini M. GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy.  Am J Hum Genet. 2016 Apr 7;98(4):627-42.

Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X,  Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW. Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Min. 2016 Apr 5; 9:13.

Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL. Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.   J Data Mining Genomics Proteomics. 2016 Jan;7(1). pii: 182. Epub 2015 Nov 8.

Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun. 2016 Feb 22;7:10740.

Rui L, Drennan AC, Ceribelli M, Zhu F, Wright GW, Xiao W, Grindle KM, Lu L, Hodson DJ, Zhao H, Xu W, Yang Y, Staudt LM.  Epigenetic gene regulation by Janus kinase 1 in diffuse large B cell lymphoma. Proc Natl Acad Sci, in press, 2016.

Smith OK, Kim RG, Fu H, Martin M, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlaine S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WC, Aladjem MI. Distinct Epigenetic Features of Differentiation-Regulated Replication Origins. Epigenetics and Chromatin 9:18. 2016.

Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan  M, Kim RG, You Y, Hanna H, Boisclair  Y, Long  Q, Aladjem  MI. A Replicator-Specific Binding Protein Essential For Site-Specific Initiation of DNA Replication in Mammalian Cells. Nat. Commun. 7:11748. 2016.

Ceribelli M, Hou EZ, Kelly PN, Huang DW, Ganapathi K, Evbuomwan MO, Pittaluga S, Shaffer AL, Wright G, Marcucci G, Forman SJ, Xiao W, Guha R, Zhang X, Ferrer M, Chaperot L, Plumas L, Jaffe ES, Thomas CJ, Reizis B, Staudt LM.  A druggable TCF4- and BRD4-dependent transcriptional network sustains malignancy in blastic plasmacytoid dendritic cell neoplasm.  Cancer Cell 2016, in press.

Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Jermusyk A, Zhang X, Rost L, Collins I, Jia J, Parikh H, Zhang T, Song L, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Bamlet WR, TCGA Research Network, Chanock S, Chatterjee N, Wolpin BM, Smith J, Olson SH, Petersen GM, Shi J, Amundadottir LT. Characterizing cis-regulatory variation in the transcriptome of histologically normal and tumor-derived pancreatic tissues. 2016: Gut

Doran AG, Wong K, Flint J, Adams DJ, Hunter KW* and Keane TM* (2016) Deep genome sequencing and variation analysis of 13 inbred mouse strains find novel missense mutations in essential DNA repair pathway genes.  Genome Biology, 17:167.

Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M.  HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res. 2016 Sep 6;44(15):7144-58. 

Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M. Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers. Genome Res. 2015 Sep;25(9):1295-308.

Deng T, Zhu ZI, Zhang S, Leng F, Cherukuri S, Hansen L, Mariño-Ramírez L, Meshorer E, Landsman D, Bustin M. HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells. Mol Cell Biol. 2013 Aug;33(16):3377-89. 

Bai L, Yang H, Hu Y, Shukla, A, Ha, N-H, Doran A, Faraji F, Goldberger N, Lee M, Keane T and Hunter KW. (2016) An integrated genome-wide systems genetics screen for breast cancer susceptibility genes.  PLoS Genetics.

Ha N-H, Long J, Cai Q, Shu X-O and Hunter KW. The circadian rhythm gene Arntl2 is a metastasis susceptibility gene for estrogen receptor-negative breast cancer.  PLoS Genetics, 12(9) e1006267.  The article highlighted by the journal (Siracusa and Bussard, PLoS Genetics 12(9) e1006299).

Kim J, Sturgill D, Tran AD, Sinclair DA, Oberdoerffer P. Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability. Nucleic Acids Res. 2016 Apr 20;44(7):e64. 

Khurana S, Kruhlak MJ, Kim J, Tran AD, Liu J, Nyswaner K, Shi L, Jailwala P, Sung MH, Hakim O, Oberdoerffer P. A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance. Nucleic Acids Res. 2016 Apr 20;44(7):e64.

2015

Young RM, Wu T, Schmitz T, Dawood M, Xiao W, Phelan JD, Xu W, Menard L, Meffre E, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza L, Staudt LM.  Survival of human lymphoma cells requires B cell receptor engagement by self-antigens.  Proc Natl Acad Sci 2015 112:13447-54.

Manna S, Kim JK, Baugé C, Cam M, Zhao Y, Shetty J, Vacchio MS, Castro E, Tran B, Tessarollo L, Bosselut R. Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation. Nat Commun. 2015;6:8152

Miles, George; Zhao, Yongmei; Levin, Yelena; et al. Multiplex Tissue and Clinical Proteomics By Next-Generation Sequencing Conference: 104th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Location: Boston, MA Date: MAR 21-27, 2015

Fu H, Martin MM, Regairaz M, Huang L, You Y, Lin CM, Ryan M, Kim R, Shimura T, Pommier Y, Aladjem MI. The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage. Nature Communications 6:6746. 2015.

Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE. Allele-specific analysis of DNA replication origins in mammalian cells. Nat Commun.6:7051. 2015.

2014

Schmitz R, Ceribelli M, Pitaluga S, Wright G, and Staudt LM.  Oncogenic mechanisms in Burkitt lymphoma. Cold Spring Harb Perspect Med. 2014 4:1-13.

Yang Y, Schmitz R, Mitala J, Whiting A, Xiao W, Ceribelli M, Wright G, Zhao H, Yang Y, Xu W, Rosenwald A, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Wiestner A, Kruhlak MJ, Iwai K, Bernal F, Staudt LM.  Essential role of the linear ubiquitin chain assembly complex in lymphoma revealed by rare germline polymorphisms.  Cancer Discovery 2014 4:480-93.

Yudkin D, Hayward B, Aladjem MI, Kumari D, Usdin K. Chromosome fragility and the abnormal replication of the FMR1 locus in Fragile X syndrome. Hum Mol Genet, 23:2940-52. 2014.

Mukhopadhyay R, Lajugie J, Fourel N, Selzer A, Schizas M, Bartholdy B, Mar J, Lin CM, Martin MM, Ryan M, Aladjem MI, Bouhassira EE. Allele-specific genome-wide profiling in human primary erythroblasts reveals replication program organization. PLoS Genetics 10(5): e1004319. 2014.

Hoskins JW, Jia J, Flandez M, Parikh H, Xiao W, Collins I, Emmanuel MA, Ibrahim A, Powell J, Zhang L, Malats N, Bamlet WR, Petersen GM, Real FX, Amundadottir LT. Transcriptome analysis of pancreatic cancer reveals a tumor suppressor function for HNF1A. Carcinogenesis 2014; 35(12): 2670-2678.

Yi, Ming; Zhao, Yongmei; Jia, Li; et al. Performance comparison of SNP detection tools with Illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. NAR Volume: 42. Issue: 12  Article Number: e101

Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM*, Cyster JG*.  Loss of signaling via Gα13 in germinal center B cell-derived lymphoma.  Nature 2014 516: 254-8.

Ceribelli M, Kelly P, Shaffer AL, Wright G, Yang Y, Mathews-Griner LA, Guha R, Shinn P, Keller JM, Liu D, Patel PR, Ferrer M, Joshi S, Nerle S, Sandy P, Normant E, Thomas CJ, Staudt LM.  Blockade of oncogenic IkB kinase activity in ABC DLBCL by small molecule BET protein inhibitors.  Proc Natl Acad Sci 2014 111:11365-70.

Nakagawa M, Schmitz R, Xiao W, Goldman CK, Xu W, Yang Y, Yu X, Waldmann TA, Staudt LM.  Gain-of-function CCR4 mutations in adult T-cell leukemia/lymphoma.  J Exp Med 2014 211:2497-2505.

2013

Xiao W, Tran B, Staudt LM, Schmitz R. High-throughput RNA sequencing in B-cell lymphomas. Methods Mol Biol 2013 971:295-312.

Jia J, Parikh H, Xiao W, Hoskins JW, Pflicke H, Liu X, Collins I, Zhou W, Wang Z, Powell J, Thorgeirsson SS, Rudloff U, Petersen GM, Amundadottir LT.  An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. BMC Med Genomics 2013; 6:33.

Fu YP, Kohaar I, Rothman N, Earl J, Figueroa JD, Ye Y, Malats N, Tang W, Liu L, Garcia-Closas M, Muchmore B, Chatterjee N, Tarway M, Kogevinas M, Porter-Gill P, Baris D, Mumy A, Albanes D, Purdue MP, Hutchinson A, Carrato A, Tardón A, Serra C, García-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Diver WR, Gapstur SM, Thun MJ, Virtamo J, Chanock SJ, Fraumeni JF Jr, Silverman DT, Wu X, Real FX, Prokunina-Olsson L. Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4974-9.

Swaminathan, Sanjay; Hu, Xiaojun; Zheng, Xin; et al. Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   Volume: 434   Issue: 2   Pages: 228-234.

Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI. Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. PLoS Genet. 9:e1003542. 2013.

Collaborative Publications 

2012

Snow AL, Xiao W, Stinson JR, Lu W, Chaigne-Delalande B, Zheng L, Pittaluga S, Matthews HF, Schmitz R, Jhavar S, Kuchen S, Kardava L, Wang W, Lamborn IT, Jing H, Raffeld M, Moir S, Fleisher TA, Staudt LM, Su HC, Lenardo MJ.  Congenital B cell lymphocytosis explained by novel germline CARD11 mutations.  J Exp Med 2012 209:2247-61.

Grontved L, Hager GL. Impact of chromatin structure on PR signaling: Transition from local to global analysis. Mol Cell Endocrinol. 357, 30-36.

Li M1, He Y, Dubois W, Wu X, Shi J, Huang J.  Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells, Molecular Cell (2012)

Yang Y, Shaffer AL, Emre NCT, Ceribelli M, Wright G, Xiao W, Powell J, Platig J, Kohlhammer H, Young RM, Zhao H, Yang Y, Xu W, Balasubramanian S, Buggy JJ, Mathews LA, Shinn P, Guha R, Ferrer M, Thomas C, Staudt LM. Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma.  Cancer Cell 2012 21:723–737.

Koh Y, Wu X, Ferris AL, Matreyek KA, Smith SJ, Lee K, KewalRamani VN, Hughes SH, Engelman A:  Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and ledgf/p75 on the efficiency and specificity of viral DNA integration. Journal of Virology. 2012. 

Wang H, Jurado KA, Wu X, Shun MC, Li X, Ferris AL, Smith SJ, Patel PA, Fuchs JR, Cherepanov P, Kvaratskheila M, Hughes SH, Engelman A: Hrp2 determines the efficiency and specificity of hiv-1 integration in ledgf/p75 knockout cells but does not contribute to the antiviral activity of a potent ledgf/p75-binding site integrase inhibitor. Nucleic acids research. 2012.

Schmitz R, Young RM, Cerribeli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson D, Buras E, Lu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Muller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI , Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM.  Pathogenetic mechanisms and therapeutic targets in Burkitt lymphoma from structural and functional genomics. Nature 2012 490:116-20.

Grontved L, Bandle R, John S, Baek S, Chung H-J, Liu Y, Aguilera G, Oberholtzer C, Hager GL, Levens D: Rapid genome-scale mapping of chromatin accessibility in tissue. Epigenetics Chromatin 2012 Jun 26;5(1):10.

2011

Ngo VN, Young RM, Schmitz R, Jhavar S, Xiao W, Lim KH, Kohlhammer H, Xu W, Yang Y, Zhao H, Shaffer AL, Romesser P, Wright G, Powell J, Rosenwald A, Muller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI , Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Staudt LM.  Oncogenically active MYD88 mutations in human lymphoma.  Nature 2011 470:115-119.

Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Research 21: 1822-1832.  2011.

CCR Sequencing Facility Presented Posters

Monika Mehta, Parimal Kumar, Vicky Chen, John Bettridge, Yongmei Zhao, Jyoti Shetty, Bao Tran. Single Cell Sequencing at CCR-Sequencing Facility. Molecular Biology in Single Cells Symposium, NCI, April 2018 & NCI Frederick Spring Research Festival, May 2018.

Keyur Talsania, Jack Chen, Tsai-wei Shen, Vicky Chen, Bao Tran, Jack Collins, Yongmei Zhao. Data Analysis for Genome Assembly and Structural Variant Detection. National Interagency Confederation for Biological Research Spring Research Festival at Fort Detrick and the National Cancer Institute, May 2018.

Vicky Chen, Tsai-wei Shen, Keyur Talsania, John Bettridge, Monika Mehta, Michael Kelly, Xiaolin Wu, Bao Tran, Jack Collins, Yongmei Zhao. High throughput Single Cell Transcriptome Sequencing Data Analysis. NIH Single Cell Symposium, April 2018.

Jack Chen, Oksana German, Sujatha Gowda, Yuliya Kriga, Christopher Hautman, Yelena Levin, Monika Mehta, Castle Raley, Jyoti Shetty, Tatyana Smirnova, Heidi Smith, Keyur Talsania, Vicky Chen, Tsai-wei Shen, Yongmei Zhao and Bao Tran. Innovative Sequencing Resources in the CCR Sequencing Facility. March 2018.

Wenming Xiao, Yongmei Zhao. A comprehensive investigation of factors impacting the accuracy of mutation detection using next-generation sequencing technology. 18-A-4219-AACR 2018.

Monika Mehta, Yongmei Zhao, Keyur Talsania, Ashley Walton, Yelena Levin, Jyoti Shetty, Elizabeth Gillanders, Bao Tran, Danielle Carrick. RNA Sequencing from Archived FFPE Tissues. AGBT Meeting, Feb 2018.

Yongmei Zhao, Keyur Talsania, Castle Raley, Monika Mehta, Jyoti Shetty, Yuliya Kriga, Sujatha Gowda, Jack Chen, Carissa Grose, Matthew Drew, Veronica Roberts, Kwong Tai Cheng, Sandra Burkett, Steffen Oeser, Robert Stephens, Daniel Soppet, Jack Collins, Bao Tran, Dominic Esposito. Draft Genome Assembly and Annotation of the Trichoplusia ni Insect Cell Line Tni-FNL. AGBT Conference 2018.

Cristobal Vera, Keyur Talsania, Ashley Walton, Sucheta Godbole, Bao Tran, Jack Collins, Yongmei Zhao. Data Analysis for Structural Variation Detection and Genome Assembly. National Interagency Confederation for Biological Research Spring Research Festival, May 2017.

Keyur Talsania, Sucheta Godbole, Ashley Walton, J. Cristobal Vera, Bao Tran, Jack Collins, Yongmei Zhao. Data Analysis Pipelines for Transcriptome Sequence Analysis. National Interagency Confederation for Biological Research Spring Research Festival, May 2017.

Monika Mehta, Yongmei Zhao, Jyoti Shetty, Castle Raley, Bao Tran. New Advancements in Next-Generation Sequencing Approaches to Address a Variety of Biological Questions. Advances in Genome Biology and Technology (AGBT) Meeting, Feb 2017.

Keyur Talsania, Sucheta Godbole, J. Cristobal Vera, Thomas Skelly, Jack Chen, Robert Stephens, Jack Collins, Bao Tran, Yongmei Zhao. Bioinformatics Support for Next-Generation Sequencing and Data Analysis at CCR-SF. National Interagency Confederation for Biological Research Spring Research Festival, May 2016.

Brenda Ho, Ashley Walton, Monika Mehta.  Analysis of Illumina library preparation protocols for NGS analysis of FFPE RNA samples in cancer research. NIH Summer Intern Poster Day at NIH Bethesda campus.  July 29th, 2016.    

Monika Mehta, Castle Raley, Yongmei Zhao, Jyoti Shetty, Bao Tran.  New Advances In Studying Cellular RNA By Next-generation Sequencing. Presented at: CCR RNA Biology Workshop at NCI Shady Grove. November 1, 2016.

CCR Sequencing Facility Presented Posters and Seminars

SF seminar Oct 28, 2020 (presentations and video recording)

Contacts

Contacts

For questions concerning the Sequencing Facility, proposal submission and funding, and project status, please contact:

Bao Tran

Bao Tran

Director, Sequencing Facility

ATRF Room D-3047
301-360-3460
bao.tran@nih.gov
Jyoti Shetty

Jyoti Shetty

Illumina Lab Manager

ATRF Room D-3038
301-360-3454
jyoti.shetty@nih.gov
Yongmei Zhao

Yongmei Zhao

Bioinformatics Manager

ATRF Room D-3048
301-360-3455
yongmei.zhao@nih.gov

Sevilay Turan

Single Cell Production Lead

ATRF Room D-3010
301-350-3454
sevilay.turan@nih.gov

Caroline Fromont

PacBio Lab Manager / R&D Scientist

ATRF Room D-3039
301-228-4799
caroline.fromont@nih.gov

Oksana German

Illumina QA Specialist

ATRF Room D-3037
301-360-3457
oksana.german@nih.gov

Yunlong He

R&D Scientist

ATRF Room D-3004
301-846-7087
yunlong.he2@nih.gov

Juanma Caravaca

ONT Lab Manager / R&D Scientist

ATRF Room D-3006
301-228-4526
juanmanuel.carava@nih.gov

Estie Schick

R&D Scientist

ATRF Room D-3004
301-360-3408
estie.schick@nih.gov

Coming Soon

New Instruments:

Revio: Newest generation long read sequencer from PacBio

  • Upgraded flow cells with 25M ZMWs (3x increase from Sequel IIe)
  • Shorter runtimes/parallel sequencing
  • On-board computation with Google DeepConsensus (>20x more computing power)
NovaSeq X Plus from Illumina

  • XLEAP-SBS chemistry – an even faster, higher quality, and more robust version of sequencing by synthesis (SBS) chemistry.
  • Ultra-high density patterned flow cell
  • Three flow cell types (1.5B, 10B and 25B) and up to 16Tb output per run (~ 3 times increase from current NovaSeq 6000)
Nabsys: High-Definition Mapping (HDM) using electronic detection of tagged single high molecular weight (HMW) DNA molecules

  • HDM provides routine, accurate, cost-effective analysis of genomic structural information, unavailable with short read technologies.
  • These characteristics make HDM an ideal first-line approach for a variety of applications for small and large genomes, including de novo map assembly, structural variant analysis, hybrid assembly, metagenome characterization and strain identification.
Xdrop-Sort: Target DNA enrichment for SV or virus integration detection

  • A novel microfluidic-based system that allows for targeted enrichment of long DNA molecules using only a few nanograms of DNA.
  • Based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted. The final product is an enriched population of DNA molecules that can be investigated by long read sequencing.
  • Single cell RNA-seq applications will be coming soon with the release of a new cartridge from Samplix.

New Applications:

Cell-free DNA sequencing: Cell-free DNA (cfDNA) refers to all non-encapsulated DNA in the bloodstream. cfDNA are nucleic acid fragments that enter the bloodstream during apoptosis or necrosis. A portion of that cell-free DNA may originate from a tumor clone and is called circulating tumor DNA (ctDNA). cfDNA sequencing will therefore provide a quick and easy way for early cancer detection. The R&D team is currently in the process of developing adapted protocols for short read and long read cfDNA sequencing.

Single cell RNA-seq on ONT with or without adaptive sampling depletion/enrichment: Single cell RNA sequencing (scRNA-seq) technology has become the state-of-the-art approach for unraveling the heterogeneity and complexity of RNA transcripts within individual cells, as well as revealing the composition of different cell types and functions within highly organized tissues/organs/organisms. ONT’s high-throughput long read sequencer, PromethION, can sequence full length cDNA generated from single cell RNA-seq captures and detect not only the gene expression, but also the isoform information at single cell level. The adaptive sampling on ONT can selectively sequence the interested genes and increase the coverage of the region of interest. Our R&D team is establishing the protocol for single cell RNA Iso-seq on ONT with or without adaptive sampling.

ResolveOME single-cell whole genome and transcriptome amplification from BioSkryb genomics: BioSkryb Genomics has developed a unified system named ResolveOME for single cell whole transcriptome and whole genome amplification sequencing analysis. The ResolveOME system allows comprehensive analysis of the transcriptome and genome in parallel from the same cell. It provides high resolution accuracy of genome analysis down to the single base level combined with the comprehensive full length mRNA transcriptome and enables the understanding of interplay of these omic layers within and between individual cells. Our R&D team is evaluating the performance of this protocol.

Illumina Complete Long Read Sequencing Technology generates contiguous long-read sequences with N50 of 5–7 kb with some reads > 10 kb. It has the potential to improve the efficiency and accuracy of some existing DNA sequencing applications while increasing the resolution of clinically important genes.The technology simplifies de novo sequencing because large repeat regions in the DNA fragments can easily be spanned.

5-hmC and 5mC Detection and Analysis: Discrimination between 5-mC and 5-hmC in CCGG sequences using enzymatic digestion and PCR amplification using the The EpiMark® 5-hmC and 5-mC Analysis Kit. This can also be used to analyze and quantitate 5-methylcytosine and 5-hydroxymethylcytosine within a specific locus.

FAQ

Coming Soon