Public Data

• Data Series	Zebrafish Zili- and Ziwi-interacting small RNAs
  Organism	Danio rerio
  Data Format/Notes	small RNA from total gonads or Argonaute IPs were cloned and sequenced using 454 GS FLX system.
  Publication Reference	Houwing S, Berezikov E, Ketting RF Zili is required for germ cell differentiation and meiosis in zebrafish. EMBO J 2008 Oct 22;27(20):2702-11. PMID: 18833190
  	Provided by the Gene Expression Omnibus
  Available Data Sets (Soft format - direct from GEO)	Ziwi-IP small RNAs from zebrafish testes; testes from adult TL Zili-IP small RNAs from zebrafish ovaries; ovary from adult TL Ziwi-IP small RNAs from zebrafish ovaries; ovary from adult TL Small RNAs from wild-type zebrafish gonads; 5 week old TL animals small RNAs from zili mutant zebrafish gonads; 5 week old hu3173 animals (TL background)
  Available Data Sets (FASTA format, more suitable for tools)	Ziwi-IP small RNAs from zebrafish testes; testes from adult TL Zili-IP small RNAs from zebrafish ovaries; ovary from adult TL Ziwi-IP small RNAs from zebrafish ovaries; ovary from adult TL Small RNAs from wild-type zebrafish gonads; 5 week old TL animals small RNAs from zili mutant zebrafish gonads; 5 week old hu3173 animals (TL background)

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• Data Series	High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and polIV mutants
  Organism	Arabidopsis thaliana
  Experiment/Experimental Treatment
  Data Format/Notes	Size fractionated small RNA from total RNA extracts was ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to 454 high throughput pyrosequencing.
  Publication Reference	Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A 2008 Feb 26;105(8):3145-50. PMID: 18287047
  	Provided by the Gene Expression Omnibus
  Available Data Sets	endogenous small RNAs from Arabidopsis thaliana col-0, wild type, flower buds endogenous small RNAs from Arabidopsis thaliana col-0, nrpd1a mutant, flower buds endogenous small RNAs from Arabidopsis thaliana col-0, nrpd1b mutant, flower buds
  Available Data Sets (FASTA format, more suitable for tools)	endogenous small RNAs from Arabidopsis thaliana col-0, wild type, flower buds endogenous small RNAs from Arabidopsis thaliana col-0, nrpd1a mutant, flower buds endogenous small RNAs from Arabidopsis thaliana col-0, nrpd1b mutant, flower buds

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• Data Series	MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype
  Experiment/Experimental Treatment
  Data Format/Notes	All arrays were condensed together using gcRMA with quantile normalization using bioconductor in R.
  Publication Reference	Chen PY, Weinmann L, Gaidatzis D, Pei Y et al. Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA 2008 Feb;14(2):263-74. PMID: 18094121
  	Provided by the Gene Expression Omnibus
  Available Data Sets	HeLa, s/as HeLa, meT-a/meT-as HeLa, meT-s/as HeLa, PIK3CB-6340 mock HeLa, PIK3CB-6340




• Data Series	Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.
  Characteristics	Plate = 2; Grade = 2; Stage = 3; Vascular Invasion = 1; NPI = 5.34; ER status = Positive; Molecular subtype = unknown
  Experiment/Experimental Treatment
  Data Format/Notes	Raw values smaller than 1 were set equal to 1. After log2 transformation probes were filtered by requiring each probe to exceed 6 in at least one sample. Systematic probe effects between plates were removed by subtracting differences between the probe median for the samples on a given plate and the probe median for all samples on both plates. Unused probes were removed and replicate probes were summarized by their mean expression profile. Two alternative between-sample normalizations were used: 1) Median centering (VALUE) The sample median was subtracted for each sample. Replicate samples were summarized by their mean expression profile. 2) Control-based normalization (CTRL_BASED_NORM) Control probes used for normalization as indicated in 'USAGE' were median centred. Sample effects were estimated by taking the mean over eight control measurements per sample. Normalization was performed by subtracting the estimated effect for each sample. Replicate samples were summarized by their mean expression profile.
  Publication Reference	Blenkiron C, Goldstein LD, Thorne NP, Spiteri I et al. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 2007;8(10):R214. PMID: 17922911
  	Provided by the Gene Expression Omnibus
  Available Data Sets	Primary breast tumour; 2390 Primary breast tumour: 2111 Primary breast tumour: 2185 Normal breast sample: N_BRST_4 Primary breast tumour: 2204

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