deepBase v3.0 download
Data generated by deepBase v3.0 can be downloaded here.
Tissue LncRNA Expression Table:
Cancer LncRNA Expression Table:
Tissue Small RNA Download Table:
| Clade |
Species |
Source |
ID |
Study |
Download |
| mammal | Mus musculus | oocytesmallRNA-19to24 | GSE10364 | Small RNA profile in fully grown mammalian oocytes | Download |
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| vertebrate | Gallus gallus | CE7 | GSE10686 | Deep sequencing of small RNA libraries from chicken embryo | Download |
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| insect | Drosophila melanogaster | WT testes (18-24nt) | GSE11086 | Deep sequencing of Drosophila melanogaster small RNAs | Download |
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| insect | Drosophila melanogaster | Imaginal disc | GSE11624 | Drosophila melanogaster small RNA sequence from 14 libraries | Download |
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| mammal | Mus musculus | mEFsmallrna_rep1 | GSE11724 | Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells | Download |
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| mammal | Mus musculus | Analysis of small RNAs in murine neutrophils cultured in vitro by Solexa/Illumina genome analyzer | GSE12075 | The impact of microRNAs on protein output | Download |
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| mammal | Mus musculus | ESC wild type (Illumina) | GSE12521 | Endogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES Cells | Download |
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| nematode | Caenorhabditis elegans | young adult males | GSE13339 | Changes in expression of microRNAs during C. elegans development | Download |
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| mammal | Homo sapiens | endogenous small RNA associated to human Argonaute 1 | GSE13370 | High-throughput pyrosequencing of endogenous small RNAs associated to human Argonaute 1 & 2 | Download |
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| deuterostome | Ciona intestinalis | Ciona Egg | GSE13625 | A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate | Download |
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| nematode | Caenorhabditis remanei | total small RNAs from C. remanei | GSE15169 | Repertoire and evolution of miRNA genes in four divergent nematode species | Download |
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| vertebrate | Gallus gallus | High-throughput sequencing of small RNAs in chicken somite embryos | GSE15513 | High-throughput sequencing of small RNAs in chicken somite embryos | Download |
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| mammal | Homo sapiens | MCF7_smallRNAseq | GSE16060 | The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs | Download |
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| mammal | Homo sapiens | Sequencing of small RNA from the H1 cell line; smRNA-seq_h1_r1 | GSE16256 | UCSD Human Reference Epigenome Mapping Project | Download |
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| mammal | Homo sapiens | smRNA-Seq analysis of H1EScd1, HS1295-1_42ERCAAXX | GSE16368 | UCSF-UBC Human Reference Epigenome Mapping Project | Download |
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| mammal | Mus musculus | NIH3T3 | GSE16579 | miRNA expression of human cancer and mouse cell lines | Download |
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| mammal | Mus musculus | 18dpp_hetero_tdrd6-KO | GSE17319 | Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members | Download |
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| insect | Bombyx mori | Whole body_primary results | GSE17965 | MicroRNAs of Bombyx mori identified by Solexa sequencing | Download |
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| mammal | Homo sapiens | Illumina: Human-superior frontal gyrus-34 days old rep1 | GSE18069 | Gene and miRNA expression data from primate postnatal brain in prefrontal cortex: time course | Download |
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| mammal | Homo sapiens | QF1160MB | GSE18381 | Characterization of the melanoma miRNAome by deep sequencing | Download |
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| mammal | Mus musculus | total RNA | GSE19172 | Mili-IP, Miwi-IP, and total RNA from mouse adult testis | Download |
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| mammal | Mus musculus | shLuc.1309 (-dox) | GSE19476 | A rapid and scalable system for studying gene function in mice using conditional RNA interference | Download |
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| mammal | Homo sapiens | Normal PBMC Sample 1 | GSE19833 | Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood | Download |
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| mammal | Mus musculus | MitoPLD+/+ E16.5 small RNA | GSE20327 | Analysis of small RNAs in piRNA pathway mutant mouse testes | Download |
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| mammal | Mus musculus | testes_rep1 | GSE20384 | Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes | Download |
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| mammal | Homo sapiens | G652T | GSE20592 | Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumors and matched controls | Download |
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| mammal | Homo sapiens | THP1_nuc_sRNAs | GSE20664 | Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans | Download |
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| mammal | Mus musculus | mouse_granulocyte_nuclei_smallRNAs | GSE20683 | RNA profiling in mouse haemopoiesis | Download |
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| mammal | Homo sapiens | fertile_donor1 | GSE21191 | Characterization of the small RNA population in Human spermatozoa | Download |
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| mammal | Homo sapiens | Human Normal Liver Tissue Sample 1 | GSE21279 | Small RNA Solexa sequencing of human liver samples | Download |
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| mammal | Mus musculus | mouse testicular tissue [09-002] | GSE21630 | Regulation of microRNA Expression and Abundance during Lymphopoiesis | Download |
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| mammal | Homo sapiens | Whole Brain small RNAs 1 | GSE22068 | Expanding the MicroRNA Targeting Code: A Novel Type of Site with Centered Pairing | Download |
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| mammal | Mus musculus | MEF_control | GSE22760 | Small RNA profiling of RNase III enzyme deficient DN3 thymocytes, Tregs, activated CD4+ T cells, and embryonic fibroblasts | Download |
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| mammal | Homo sapiens | Mututated CLL (CLLM633) | GSE22898 | Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs | Download |
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| nematode | Caenorhabditis elegans | small RNAs from C. elegans, wild-type, day 0 of adulthood | GSE24510 | Deep sequencing of small RNAs from C. elegans during aging | Download |
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| mammal | Mus musculus | paternal control diet 3 | GSE25899 | Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals | Download |
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| mammal | Mus musculus | HL1_siNon_smallRNAseq | GSE26397 | The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5 and Srf, Histone Modifications and MicroRNAs | Download |
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| mammal | Sus scrofa | 2268 AF, small RNA | GSE26572 | A 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 sequencing | Download |
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| mammal | Homo sapiens | HeLa ELAV1/HuR sRNA siRNA1 | GSE29943 | Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP | Download |
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| mammal | Homo sapiens | Skin psoriasis involved 1 | GSE31037 | Small RNA sequencing in normal and psoriatic skin | Download |
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| mammal | Homo sapiens | Normal skin1 | GSE36236 | Small RNA sequencing of melanoma samples to deduce microRNA expression profiles | Download |
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| mammal | Homo sapiens | embryonal tumor A17 | GSE39841 | YM500: An integrative small RNA sequencing (smRNA-seq) database for microRNA research | Download |
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| nematode | Caenorhabditis remanei | C. remanei adult females+males | GSE41461 | Analysis of miRNA, piRNA and siRNA in Caenorhabditis species | Download |
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| mammal | Homo sapiens | Normal Brain 2 | GSE43335 | Small RNA-seq of undiseased human brain | Download |
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| mammal | Homo sapiens | control sample 0 | GSE46579 | A blood based 12-miRNA signature of Alzheimer patients | Download |
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| mammal | Mus musculus | Abundance of piRNAs in mouse testes | GSE5026 | Characterization of the piRNA Complex from Rat Testes | Download |
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| nematode | Caenorhabditis elegans | MIT/WI Bartel C.elegans 454 2006 | GSE5990 | High-throughput sequencing of small RNAs from Caenorhabditis elegans | Download |
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| mammal | Mus musculus | Developmentally regulated piRNA clusters implicate MILI in transposon control | GSE7414 | Developmentally regulated piRNA clusters implicate MILI in transposon control | Download |
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| insect | Drosophila melanogaster | imaginal discs | GSE7448 | High-throughput sequencing of small RNAs from Drosophila | Download |
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| mammal | Homo sapiens | heart | SRA012516 | The small RNA component from 2 individuals across 8 tissues | Download |
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| mammal | Homo sapiens | blood_leukemia | SRA029149 | Raw sequencing data for the MLL-rearranged precursor B-ALL-representing library | Download |
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Cancer Small RNA Download Table:
Exosomes RNA Download Table:
tRFs Annotation Download Table: