Data Sets

Ge, D.T., Tipping, C., Brodsky, M.H., Zamore, P.D. (2016). Rapid screening for CRISPR-directed editing of the Drosophila genome using white co-conversion. Genes, Genomes, Genetics, 19 August, epub ahead of print. 

Ouimet, M., Koster, S., Sakowski, E., Ramkhelawon, B., van Solingen, C., Oldebeken, S., Karunakaran, D., Portal-Celhay, C., Sheedy, F.J., Ray, T.D., Cecchini, K., Zamore, P.D., Yaner, K.J., Marcel, Y.L., Philips J.A., and Moore, K.J. (2016). Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism. Nature Immunology 17, 677-686. (PMCID:PMC4873392).

Han, B.W., Wang, W., Li, C., Weng, Z., Zamore, P.D. (2015). Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 348, 817-821. (PMCID:PMC4545291).

  • Sequencing Data from the NCBI Sequence Read Archive can be found here.

Roy, C.K., Olson, S., Graveley, B.R., Zamore, P.D., Moore, M.J. (2015). Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation. eLife 13, 1-21. (PMCID: PMC4442144).

  • The NCBI Short Read Archive accession number for sequencing data can be found here.

Wang, W., Yoshikawa, M., Han, B.W., Izumi, N., Tomari, Y., Weng, Z., Zamore, P.D. (2014). The Initial Uridine of Primary piRNAs Does not Create the Tenth Adenine that is the Hallmark of Secondary piRNAs. Molecular Cell 56, 708-716. (PMCID: PMC4337030).

Fukunaga, R., Colpan, C., Han, B.W., Zamore, P.D. (2014). Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO Journal, 33, 371-384. (PMCID: PMC3989643).

  • The SRA accession number (SRX337129) for the small RNA libraries reported in this paper can be found here.

Zhang, Z., Koppetsch, B.S., Wang, J.W., Tipping, C., Weng, Z.W., Theurkauf, W.E., Zamore, P.D. (2013). Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the tudor domain protein Qin. EMBO Journal 33, 536-539 (PMCID: PMC3989468).

Li, X.Z., Roy, C.K., Dong, X., Bolcun-Filas, E., Wang, J., Han, B.W., Xu, J., Moore, M.J., Schimenti, J.C., Weng, Z., Zamore, P.D. (2013). An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes. Molecular Cell, 50, 67-81. (PMCID: PMC3671569).

  • Supplemental material can be found here.
  • The Gene Expression Omnibus (GEO) accession number for the RNA-seq, ChIP-seq, and small RNA data reported in this paper is GSE44690.  The information can be found here.
  • piRNA transcripts by type can be found here.
  • Rooster piRNA cluster coordinates, Gg3 genome.

Zhang F., Wang J., Xu J., Zhang Z., Koppetsch B.S., Schultz N., Vreven T., Meignin C., Davis I., Zamore P.D., Weng Z., Theurkauf W.E. (2012). UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery. Cell 151, 871-884. (PMCID: PMC3499805).

Fukunaga, R., Han, B,W., Hung, J.-H., Xu, J., Weng, Z., Zamore, P.D. (2012). Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell, 151, 533-546. (PMCID: PMC3609301).

  • Download the RNA-seq library information for accesseion number SRP014526 from here.
  • Supplemental material can be found here.
  • Download GSE accesion number data for GSE37443 from the NCBI Gene Expression Omnibus

Xie, J., Ameres, S.L., Friedline, R., Hung, J.-H., Zhang, Y., Xie, Q., Zhong, L., Zhang, H., Su, Q., He, R., Li, M., Mu, X., Broderick, J.A., Li, C., Kim, J., Weng, Z., Flotte, T.R., Zamore, P.D., Gao, G. (2012). Long-term, efficient inhibition of miRNA function in mice using Tough Decoys delivered by Adeno-associated virus vectors. Nature Methods 9, 403-409. (PMCID: PMC3420816).

Zhang, Z., Xu, J., Koppetsch, B.S., Wang, J., Tipping, C., Ma, S., Weng, Z., Theurkauf, W.E., Zamore, P.D. (2011). Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3-ligase and Tudor Domains. Molecular Cell137, 1551-1563. (PMCID: PMC3236501).

Han, B.W., Hung, J.-H.,Weng, Z., Zamore, P.D., and Ameres, S.L. (2011). The 3′ to 5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1. Current Biology 21, 1878-1887. (PMCID: PMC3236499).

  •  Download sequencing data for accession number GSE31689 here.

Berezikov E., Robine N., Samsonova A., Westholm J.O., Naqvi A., Hung J.H., Okamura K., Dai Q., Bortolamiol-Becet D., Martin R., Zhao Y., Zamore P.D., Hannon G.J., Marra M.A., Weng Z., Perrimon N., and Lai E.C. (2011). Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research 21, 203-15. (PMCID:PMC3032924).

  •  Download the small RNA data sets here.

Carone B.R., Fauquier L., Habib N., Shea J.M., Hart C.E., Li R., Bock C., Li C., Gu H., Zamore P.D., Meissner A., Weng Z., Hofmann H.A., Friedman N., and Rando O.J. (2010). Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell 143, 1084-96. (PMCID: PMC3039484).

Ameres, S.L., Horwich, M.D., Hung, J., Xu, J., Ghildiyal, M., Weng, Z., and Zamore, P.D. (2010). Target RNA-directed trimming and tailing of small silencing RNAs. Science 328, 1534-1539. (PMCID: PMC2902985).

  •  Download sequence data from the NCBI Short Read Archive here.

Ghildiyal, M., Xu, J., Seitz, H., Weng, Z., and Zamore, P.D. (2010). Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43-56. (PMCID: PMC2802036).

  •  Download sequencing data sets for GSE18806 from the National Center for Biotechnology Information Short Read Archive here.

Kadener, S., Menet, J.S., Sugino, K., Horwich, M.D., Weissbein, U., Nawathean, P., Vagin, V.V., Zamore, P.D., Nelson, S.B., and Rosbash, M. (2009).  A role for microRNAs in the Drosophila circadian clock. Genes & Development 23, 2179-2191. (PMCID: PMC2751990).

Klattenhoff, C., X, H., Li, C., Lee, S., Xu, J., Khurana, J., Schultz, N., Koppetsch, B.S., Nowosielska, A., Seitz, H., Zamore, P.D., Weng, Z., and Theurkauf, W.E. (2009). The Drosophila HP1 homologue Rhino is required for transposon silencing and piRNA production by dual strand clusters. Cell 138, 1137-1149. (PMCID:PMC2770713).

 Li, C., Vagin, V. V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M. D., Syrzycka, M., Honda, B. M., Kittler, E. L., Zapp, M. L., Klattenhoff, C., Schulz, N., Theurkauf, W. E., Weng, Z., and Zamore, P. D. (2009) Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies. Cell 132, 509-521. (PMCID: PMC2768572).

Ghildiyal, M., Seitz, H., Horwich, M. D., Li, C., Du, T., Lee, S., Xu, J., Kittler, E. L., Zapp, M. L., Weng, Z., and Zamore, P. D. (2008) Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells. Science 320, 1077-1081. (PMCID: PMC2953241).

Seitz, H., Ghildiyal, M., and Zamore, P. D. (2008) Argonaute Loading Improves the 5' Precision of Both MicroRNAs and Their miRNA* Strands in Flies. Current Biology 18, 147-151. (PMCID: PMC2854039).

Vagin, V. V., Sigova, A., Li, C., Seitz, H., Gvozdev, V., and Zamore, P. D. (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320-324.

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