Overview
CCR Sequencing Facility
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
tranb2@mail.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.
Long-reads/PacBio sequencing:
- 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
- Targeted Sequencing – long amplicon sequencing; full-length viral sequencing full-length vector sequencing, targeted enrichment, and multiplexing strategies
Others:
- Whole Genome Sequencing using 10X Genomics Linked-Reads: Long-range information from short-read sequencing, to resolve genic phasing, reveal structural variation and detect variants in complex genomic regions.
- Exome Sequencing using 10X Genomics Linked-Reads: Large scale structural variants detection across the entire exome.
- Optical mapping using Bionano Technology: Imaging and analysis of extremely long, high-molecular-weight DNA felicitates identification of structural variants and creation of de novo genome assemblies
Single-cell sequencing:
- Single Cell Transcriptomics: 3’ and 5’ gene expression profiling to uncover cell-to-cell gene expression variability
- Single Cell Immune Profiling: simultaneous analysis of the cellular context of the adaptive immune response and immune repertoires of thousands of T and B cells
- Single Cell ATAC-seq: chromatin profiling of thousands of single cells to provide insights into the regulatory landscape of the genome
- Single Cell CNV analysis: single cell CNV calls at 2 Mb resolution for revealing genome heterogeneity
R&D resources:
New applications, new protocols, new platforms etc.
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.
Pricing
Illumina Library Construction | CCR | NIAID | Other Divisions |
Project Type | Library Prep Per Sample | Library Prep Per Sample | Library Prep Per Sample |
ChIP-Seq | $50 + (Sequencing Cost) | $108 + (Sequencing Cost) | $94 + (Sequencing Cost) |
gDNA-Seq | $29 + (Sequencing Cost) | $77 + (Sequencing Cost) | $55 + (Sequencing Cost) |
Nextera DNA Flex | $38 + (Sequencing Cost) | $90 + (Sequencing Cost) | $71 + (Sequencing Cost) |
Whole Genome Methyl-Seq | $58 + (Sequencing Cost) | $120 + (Sequencing Cost) | $109 + (Sequencing Cost) |
Total RNA-Seq | $106 + (Sequencing Cost) | $191 + (Sequencing Cost) | $198 + (Sequencing Cost) |
mRNA-Seq | $80 + (Sequencing Cost) | $152 + (Sequencing Cost) | $149 + (Sequencing Cost) |
miRNA-Seq | $56 + (Sequencing Cost) | $117 + (Sequencing Cost) | $105 + (Sequencing Cost) |
10XChromium Library Construction | CCR | NIAID | Other Divisions |
Project Type | Library Prep Per Sample | Library Prep Per Sample | Library Prep Per Sample |
10XChromium Single Cell 3′ RNA-Seq (v3) | $1500 + (Sequencing Cost) | $1533 + (Sequencing Cost) | $1875 + (Sequencing Cost) |
10XChromium Single Cell 3′ RNA-Seq + feature barcode | $1550 + (Sequencing Cost) | $1583 + (Sequencing Cost) | $1938 + (Sequencing Cost) |
10XChromium Single Cell 5′ RNA-Seq | $1500 + (Sequencing Cost) | $1533 + (Sequencing Cost) | $1875 + (Sequencing Cost) |
10XChromium Single Cell VDJ | $1500 + (Sequencing Cost) | $1533 + (Sequencing Cost) | $1875 + (Sequencing Cost) |
10XChromium Single Cell VDJ 5′ GEX | $1600 + (Sequencing Cost) | $1633 + (Sequencing Cost) | $2000 + (Sequencing Cost) |
10XChromium Single Cell ATAC-seq | $1375 + (Sequencing Cost) | $1408 + (Sequencing Cost) | $1719 + (Sequencing Cost) |
10XChromium Single Cell CNV (16 Reaction Kit) | $1500 + (Sequencing Cost) | $1533 + (Sequencing Cost) | $1875 + (Sequencing Cost) |
10XChromium Single Cell CNV (4 Reaction Kit) | $1600 + (Sequencing Cost) | $1633 + (Sequencing Cost) | $2000 + (Sequencing Cost) |
Illumina NovaSeq | CCR | NIAID | Other Divisions |
Run Type | Cost Per Lane | Cost Per Lane | Cost Per Lane |
S1 x 100 bp | $3310 + (Lib. Prep) | $4940 + (Lib. Prep) | $6175 + (Lib. Prep) |
S1 x 200 bp | $4248 + (Lib. Prep) | $6340 + (Lib. Prep) | $7925 + (Lib. Prep) |
S1 x 300 bp | $4985 + (Lib. Prep) | $7440 + (Lib. Prep) | $9300 + (Lib. Prep) |
S2 x 100 bp | $6928 + (Lib. Prep) | $10340 + (Lib. Prep) | $12925 + (Lib. Prep) |
S2 x 200 bp | $9273 + (Lib. Prep) | $13840 + (Lib. Prep) | $17300 + (Lib. Prep) |
S2 x 300 bp | $10780 + (Lib. Prep) | $16090 + (Lib. Prep) | $20113 + (Lib. Prep) |
S4 x 200 bp | $18452 + (Lib. Prep) | $27540 + (Lib. Prep) | $34425 + (Lib. Prep) |
S4 x 300 bp | $21185 + (Lib. Prep) | $31620 + (Lib. Prep) | $39525 + (Lib. Prep) |
SP x 100 bp | $2070 + (Lib. Prep) | $3090 + (Lib. Prep) | $3863 + (Lib. Prep) |
SP x 300 bp | $3142 + (Lib. Prep) | $4690 + (Lib. Prep) | $5863 + (Lib. Prep) |
SP x 500 bp | $4248 + (Lib. Prep) | $6340 + (Lib. Prep) | $7925 + (Lib. Prep) |
XP 2-Lane Kit | $299 + (Lib. Prep) | $299 + (Lib. Prep) | $299 + (Lib. Prep) |
XP 4-Lane Kit | $999 + (Lib. Prep) | $999 + (Lib. Prep) | $999 + (Lib. Prep) |
MiSeq | CCR | NIAID | Other Divisions |
Run Type | Cost | Cost | Cost |
SR 1 x 50 bp (V2) | $563 + (Lib. Prep) | $840 + (Lib. Prep) | $1050 + (Lib. Prep) |
PE 2 x 150 bp (V2) | $723 + (Lib. Prep) | $1080 + (Lib. Prep) | $1350 + (Lib. Prep) |
PE 2 x 250 bp (V2) | $811 + (Lib. Prep) | $1210 + (Lib. Prep) | $1513 + (Lib. Prep) |
PE 2 x 75 bp (V3) | $623 + (Lib. Prep) | $930 + (Lib. Prep) | $1163 + (Lib. Prep) |
PE 2 x 300 bp (V3) | $1058 + (Lib. Prep) | $1580 + (Lib. Prep) | $1975 + (Lib. Prep) |
Illumina NextSeq High Output | CCR | NIAID | Other Divisions |
Run Type | Cost | Cost | Cost |
1 x 75 bp (V2) | $1022 + (Lib. Prep) | $1525 + (Lib. Prep) | $1906 + (Lib. Prep) |
2 x 75 bp (V2) | $1956 + (Lib. Prep) | $2920 + (Lib. Prep) | $3650 + (Lib. Prep) |
2 x 150 bp (V2) | $3136 + (Lib. Prep) | $4680 + (Lib. Prep) | $5850 + (Lib. Prep) |
Pacbio Sequel Sample Prep | CCR | NIAID | Other Divisions |
Project Type | Library Prep Per Sample | Library Prep Per Sample | Library Prep Per Sample |
gDNA | $94 + (Sequencing Cost) | $143 + (Sequencing Cost) | $179 + (Sequencing Cost) |
gDNA Low Input | $57 + (Sequencing Cost) | $86 + (Sequencing Cost) | $108 + (Sequencing Cost) |
Microbial, Multiplexed | $53 + (Sequencing Cost) | $81 + (Sequencing Cost) | $101 + (Sequencing Cost) |
Amplicon, Single or Multiplexed | $18 + (Sequencing Cost) | $27 + (Sequencing Cost) | $34 + (Sequencing Cost) |
Iso-Seq, Single | $84 + (Sequencing Cost) | $127 + (Sequencing Cost) | $159 + (Sequencing Cost) |
Iso-Seq, Multiplexed | $37 (Multiplexing Per Library) + (Sequencing Cost) | $56 (Multiplexing Per Library) + (Sequencing Cost) | $70 (Multiplexing Per Library) + (Sequencing Cost) |
HLA Sequencing | $25 + (Sequencing Cost) | $38 + (Sequencing Cost) | $48 + (Sequencing Cost) |
*Note: All prices above are per sample
**Note: Iso-Seq price is based on whole transcriptome amplification and sequencing; estimates for targeted Iso-Seq will be determined individually |
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Pacbio Sequel Sequencing | CCR | NIAID | Other Divisions |
Run Type | Cost | Cost | Cost |
SMRT Cell 1M V2 | $589 + (Lib. Prep) | $892 + (Lib. Prep) | $1115 + (Lib. Prep) |
SMRT Cell 1M V2 LongRead (LR) | $589 + (Lib. Prep) | $892 + (Lib. Prep) | $1115 + (Lib. Prep) |
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 |
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Illumina | PacBio |
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Protocols and Workflows |
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Illumina | PacBio |
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Publications
Publications
2019
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. doi: 10.1016/j.immuni.2019.06.023. 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).
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.
Zhao Y*, Mehta M*, Walton A*, Talsania K*, Levin Y, Shetty J, Gillanders EM, Tran B, and Carrick D. Robustness of RNA sequencing on older formalin-fixed paraffin-embedded tissue from high-grade ovarian serous adenocarcinomas. (*equal contribution) Manuscript under review
2018
Zheng H,
Collaborative Publications
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
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
Thompson,
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
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,
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
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-
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
Ha N-H, Long J, Cai Q, Shu X-O
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
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,
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,
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.
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
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
Schmitz R, Young RM,
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-
Vicky Chen, Tsai-
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-
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.
Contacts
Contacts
For questions concerning the Sequencing Facility, proposal submission and funding, and project status, please contact:
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![]() Christopher Lyons (Hautman)Acting PacBio Lab ManagerATRF Room D-3039 |
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R&D/Coming Soon
Oxford Nanopore Technologies MinIon Sequencing
- Sequencing via nanopore technology enables rapid identification of ultra-long reads, with average yields 0.5 – 10 Gb per flow cell, depending on which application utilizes
- Read lengths averaging greater than 100,000 bases per molecule, with maximum read lengths > 1,000,000 bases, facilitate genome assembly and mapping of repetitive regions
- Amplification-free direct sequencing of individual DNA and RNA molecules precludes PCR bias and artifacts
- Minimal machine turnaround time provides flexibility in experimental and run design