rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
37994,SRR1265763,SRX529157,SRS598854,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Eye Replicate 3 sRNAseq,GSM1376646,,source name:Eye|tissue:Eye|genetic background:Wild type   Singapore strain,Eye Replicate 3 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Eye,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,tissue:Eye|genetic background:Wild type   Singapore strain,GSM1376646,GSM1376646: Eye Replicate 3 sRNAseq; Danio rerio; miRNA Seq,GSM1376646,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376646,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZE014_GCCAAT_L005_R1.fastq.gz,fastq,299134784.0,3935984.0,GSM1376646 r1,0:76,A:62089027;C:82689882;G:78294122;T:76032871;N:28882,76,,,,62089027,82689882,78294122,76032871,28882,SRX529157,SRS598854,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00078,,8e-05,,0.99892,,0.66406,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Eye,Sensory System
37995,SRR1265762,SRX529156,SRS598853,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Eye Replicate 2 sRNAseq,GSM1376645,,source name:Eye|tissue:Eye|genetic background:Wild type   Singapore strain,Eye Replicate 2 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Eye,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,tissue:Eye|genetic background:Wild type   Singapore strain,GSM1376645,GSM1376645: Eye Replicate 2 sRNAseq; Danio rerio; miRNA Seq,GSM1376645,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376645,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZE013_ACAGTG_L005_R1.fastq.gz,fastq,622465080.0,8190330.0,GSM1376645 r1,0:76,A:127621827;C:166524813;G:172833628;T:155425094;N:59718,76,,,,127621827,166524813,172833628,155425094,59718,SRX529156,SRS598853,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00132,,7e-05,,0.99886,,0.66956,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Eye,Sensory System
37996,SRR1265761,SRX529155,SRS598852,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Eye Replicate 1 sRNAseq,GSM1376644,,source name:Eye|tissue:Eye|genetic background:Wild type   Singapore strain,Eye Replicate 1 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Eye,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,tissue:Eye|genetic background:Wild type   Singapore strain,GSM1376644,GSM1376644: Eye Replicate 1 sRNAseq; Danio rerio; miRNA Seq,GSM1376644,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376644,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZE008_TGACCA_L005_R1.fastq.gz,fastq,906617148.0,11929173.0,GSM1376644 r1,0:76,A:188700519;C:246755919;G:238402849;T:232669963;N:87898,76,,,,188700519,246755919,238402849,232669963,87898,SRX529155,SRS598852,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00073,,4e-05,,0.9991,,0.61788,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Eye,Sensory System
38046,SRR1427469,SRX612649,SRS643610,SRP043465,PRJNA253203,Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration,GSE58702,Transcriptome Analysis,Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified  the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs  microRNAs miRNAs  that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration  we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration  we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs  we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before  during and post completion of zebrafish retinal regeneration,,pubmed:25220904,,28d,GSM1417152,,source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,28d,Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al.  2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level,Retina,,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,,strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,GSM1417152,GSM1417152: 28d; Danio rerio; miRNA Seq,GSM1417152,,1,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,GEO Accession:GSM1417152,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP043465,,,28d.fq,bam,694299184.0,32089203.0,GSM1417152 r1,0:21.64 1:0,A:174747494;C:132129648;G:193085254;T:194336788;N:0,21,0,,,174747494,132129648,193085254,194336788,0,SRX612649,SRS643610,SRA171872,GEO,"Biological Sciences, Vanderbilt University",1,0.93434,,0.05272,,0.98831,,0.56642,,23,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2014-06-20,Adult,Adult,Eye,Sensory System
38047,SRR1427468,SRX612648,SRS643609,SRP043465,PRJNA253203,Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration,GSE58702,Transcriptome Analysis,Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified  the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs  microRNAs miRNAs  that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration  we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration  we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs  we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before  during and post completion of zebrafish retinal regeneration,,pubmed:25220904,,72h,GSM1417151,,source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,72h,Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al.  2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level,Retina,,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,,strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,GSM1417151,GSM1417151: 72h; Danio rerio; miRNA Seq,GSM1417151,,1,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,GEO Accession:GSM1417151,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP043465,,,72h.fq,fastq,689263089.0,31419317.0,GSM1417151 r1,0:21.94 1:0,A:161567060;C:125003691;G:193763870;T:208928468;N:0,21,0,,,161567060,125003691,193763870,208928468,0,SRX612648,SRS643609,SRA171872,GEO,"Biological Sciences, Vanderbilt University",1,0.93237,,0.03751,,0.98774,,0.51765,,20,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2014-06-20,Adult,Adult,Eye,Sensory System
38048,SRR1427467,SRX612647,SRS643608,SRP043465,PRJNA253203,Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration,GSE58702,Transcriptome Analysis,Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified  the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs  microRNAs miRNAs  that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration  we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration  we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs  we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before  during and post completion of zebrafish retinal regeneration,,pubmed:25220904,,0h,GSM1417150,,source name:Retina|strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,0h,Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al.  2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level,Retina,,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,,strain:albino alb / |age:adult|genotype:wildtype|tissue:retina,GSM1417150,GSM1417150: 0h; Danio rerio; miRNA Seq,GSM1417150,,1,Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected  ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al.  2012. Libraries were constructed following the protocol published by Wei et al.  2012,GEO Accession:GSM1417150,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP043465,,,0h.bam,fastq,3005859202.0,134278309.0,GSM1417150 r1,0:22.39,A:762111385;C:628084257;G:836553469;T:779110091;N:0,22,,,,762111385,628084257,836553469,779110091,0,SRX612647,SRS643608,SRA171872,GEO,"Biological Sciences, Vanderbilt University",1,0.94362,,0.03903,,0.99093,,0.5848,,22,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2014-06-20,Adult,Adult,Eye,Sensory System
39613,SRR1873567,SRX915247,SRS870227,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,eyes,GSM1630511,,source name:adult eyes 1 year old|strain/background:AB|genotype/variation:wild type|tissue:eyes|developmental stage:adult|age:1 year,eyes,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult eyes 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:eyes|developmental stage:adult|age:1 year,GSM1630511,GSM1630511: eyes; Danio rerio; miRNA Seq,GSM1630511,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630511,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,173069.0,3135.0,GSM1630511 r1,0:4 1:51.21,A:50732;C:44705;G:40960;T:36324;N:348,4,51,,,50732,44705,40960,36324,348,SRX915247,SRS870227,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,52,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Eye,Sensory System