• Data generated by deepBase v2.0 or publications can be downloaded as follows:
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    LncRNA Expression Table:

    Clade Species Download
    mammalHomo sapiensDownload
    mammalPan troglodytesDownload
    mammalGorilla gorilla gorillaDownload
    mammalMacaca mulattaDownload
    mammalMus musculusDownload
    mammalRattus norvegicusDownload
    mammalBos taurusDownload
    mammalMonodelphis domesticaDownload
    mammalOrnithorhynchus anatinusDownload
    vertebrateGallus gallusDownload
    vertebrateXenopus tropicalisDownload
    vertebrateDanio rerioDownload
    insectDrosophila melanogasterDownload
    nematodeCaenorhabditis elegansDownload
       

    LncRNA Download Table (bed format):

    Clade Species Download
    mammalHomo sapiensDownload
    mammalPan troglodytesDownload
    mammalGorilla gorilla gorillaDownload
    mammalMacaca mulattaDownload
    mammalMus musculusDownload
    mammalRattus norvegicusDownload
    mammalBos taurusDownload
    mammalMonodelphis domesticaDownload
    mammalOrnithorhynchus anatinusDownload
    vertebrateGallus gallusDownload
    vertebrateXenopus tropicalisDownload
    vertebrateDanio rerioDownload
    insectDrosophila melanogasterDownload
    nematodeCaenorhabditis elegansDownload
       

    Small RNA Download Table:

    Clade Species Source ID Study Download
    mammalMus musculusoocytesmallRNA-19to24GSE10364Small RNA profile in fully grown mammalian oocytesDownload
    vertebrateGallus gallusCE7GSE10686Deep sequencing of small RNA libraries from chicken embryoDownload
    insectDrosophila melanogasterWT testes (18-24nt)GSE11086Deep sequencing of Drosophila melanogaster small RNAsDownload
    insectDrosophila melanogasterImaginal discGSE11624Drosophila melanogaster small RNA sequence from 14 librariesDownload
    mammalMus musculusmEFsmallrna_rep1GSE11724Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cellsDownload
    mammalMus musculusAnalysis of small RNAs in murine neutrophils cultured in vitro by Solexa/Illumina genome analyzerGSE12075The impact of microRNAs on protein outputDownload
    mammalMus musculusESC wild type (Illumina)GSE12521Endogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES CellsDownload
    nematodeCaenorhabditis elegansyoung adult malesGSE13339Changes in expression of microRNAs during C. elegans developmentDownload
    mammalHomo sapiensendogenous small RNA associated to human Argonaute 1GSE13370High-throughput pyrosequencing of endogenous small RNAs associated to human Argonaute 1 & 2Download
    deuterostomeCiona intestinalisCiona EggGSE13625A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordateDownload
    nematodeCaenorhabditis remaneitotal small RNAs from C. remaneiGSE15169Repertoire and evolution of miRNA genes in four divergent nematode speciesDownload
    vertebrateGallus gallusHigh-throughput sequencing of small RNAs in chicken somite embryosGSE15513High-throughput sequencing of small RNAs in chicken somite embryosDownload
    mammalHomo sapiensMCF7_smallRNAseqGSE16060The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAsDownload
    mammalHomo sapiensSequencing of small RNA from the H1 cell line; smRNA-seq_h1_r1GSE16256UCSD Human Reference Epigenome Mapping ProjectDownload
    mammalHomo sapienssmRNA-Seq analysis of H1EScd1, HS1295-1_42ERCAAXXGSE16368UCSF-UBC Human Reference Epigenome Mapping ProjectDownload
    mammalMus musculusNIH3T3GSE16579miRNA expression of human cancer and mouse cell linesDownload
    mammalMus musculus18dpp_hetero_tdrd6-KOGSE17319Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family membersDownload
    insectBombyx moriWhole body_primary resultsGSE17965MicroRNAs of Bombyx mori identified by Solexa sequencingDownload
    mammalHomo sapiensIllumina: Human-superior frontal gyrus-34 days old rep1GSE18069Gene and miRNA expression data from primate postnatal brain in prefrontal cortex: time courseDownload
    mammalHomo sapiensQF1160MBGSE18381Characterization of the melanoma miRNAome by deep sequencingDownload
    mammalMus musculustotal RNAGSE19172Mili-IP, Miwi-IP, and total RNA from mouse adult testisDownload
    mammalMus musculusshLuc.1309 (-dox)GSE19476A rapid and scalable system for studying gene function in mice using conditional RNA interferenceDownload
    mammalHomo sapiensNormal PBMC Sample 1GSE19833Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral bloodDownload
    mammalMus musculusMitoPLD+/+ E16.5 small RNAGSE20327Analysis of small RNAs in piRNA pathway mutant mouse testesDownload
    mammalMus musculustestes_rep1GSE20384Mammalian microRNAs: Experimental evaluation of novel and previously annotated genesDownload
    mammalHomo sapiensG652TGSE20592Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumors and matched controlsDownload
    mammalHomo sapiensTHP1_nuc_sRNAsGSE20664Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoansDownload
    mammalMus musculusmouse_granulocyte_nuclei_smallRNAsGSE20683RNA profiling in mouse haemopoiesisDownload
    mammalHomo sapiensfertile_donor1GSE21191Characterization of the small RNA population in Human spermatozoaDownload
    mammalHomo sapiensHuman Normal Liver Tissue Sample 1GSE21279Small RNA Solexa sequencing of human liver samplesDownload
    mammalMus musculusmouse testicular tissue [09-002]GSE21630Regulation of microRNA Expression and Abundance during LymphopoiesisDownload
    mammalHomo sapiensWhole Brain small RNAs 1GSE22068Expanding the MicroRNA Targeting Code: A Novel Type of Site with Centered PairingDownload
    mammalMus musculusMEF_controlGSE22760Small RNA profiling of RNase III enzyme deficient DN3 thymocytes, Tregs, activated CD4+ T cells, and embryonic fibroblastsDownload
    mammalHomo sapiensMututated CLL (CLLM633)GSE22898Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAsDownload
    nematodeCaenorhabditis eleganssmall RNAs from C. elegans, wild-type, day 0 of adulthoodGSE24510Deep sequencing of small RNAs from C. elegans during agingDownload
    mammalMus musculuspaternal control diet 3GSE25899Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammalsDownload
    mammalMus musculusHL1_siNon_smallRNAseqGSE26397The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5 and Srf, Histone Modifications and MicroRNAsDownload
    mammalSus scrofa2268 AF, small RNAGSE26572A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencingDownload
    mammalHomo sapiensHeLa ELAV1/HuR sRNA siRNA1GSE29943Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIPDownload
    mammalHomo sapiensSkin psoriasis involved 1GSE31037Small RNA sequencing in normal and psoriatic skinDownload
    mammalHomo sapiensNormal skin1GSE36236Small RNA sequencing of melanoma samples to deduce microRNA expression profilesDownload
    mammalHomo sapiensembryonal tumor A17GSE39841YM500: An integrative small RNA sequencing (smRNA-seq) database for microRNA researchDownload
    nematodeCaenorhabditis remaneiC. remanei adult females+malesGSE41461Analysis of miRNA, piRNA and siRNA in Caenorhabditis speciesDownload
    mammalHomo sapiensNormal Brain 2GSE43335Small RNA-seq of undiseased human brainDownload
    mammalHomo sapienscontrol sample 0GSE46579A blood based 12-miRNA signature of Alzheimer patientsDownload
    mammalMus musculusAbundance of piRNAs in mouse testesGSE5026Characterization of the piRNA Complex from Rat TestesDownload
    nematodeCaenorhabditis elegansMIT/WI Bartel C.elegans 454 2006GSE5990High-throughput sequencing of small RNAs from Caenorhabditis elegansDownload
    mammalMus musculusDevelopmentally regulated piRNA clusters implicate MILI in transposon controlGSE7414Developmentally regulated piRNA clusters implicate MILI in transposon control Download
    insectDrosophila melanogasterimaginal discsGSE7448High-throughput sequencing of small RNAs from DrosophilaDownload
    mammalHomo sapiensheartSRA012516The small RNA component from 2 individuals across 8 tissuesDownload
    mammalHomo sapiensblood_leukemiaSRA029149Raw sequencing data for the MLL-rearranged precursor B-ALL-representing libraryDownload
       

    circular RNA Download Table:

    Clade Species Download
    mammalHomo sapiensDownload
    mammalMus musculusDownload
    nematodeCaenorhabditis elegansDownload
    insectDrosophila melanogasterDownload
       

    Software Download Table:

    Version File Platform Package Type Download
    1.0snoSeekerNGS.msiWindowsGUI (Graphic User Interface)Download
    1.0snoSeekerNGS-1.0.zipWindowsBinary distribution for Win32Download
    1.0snoSeekerNGS-1.0.tar.gzLinuxBinary distribution for linuxDownload