{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"size fractionation\" and tissue_curation = \"Brain\"", "rows": [[32926, "SRR29498570", "SRX25008882", "SRS21709101", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.", null, null, null, null, "M2b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M2b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "07", "07", "Total RNA was extracted from different zebrafish tissues using TRIzol reagent. 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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.", null, "pubmed:26574018", null, "Female Brain Replicate 3 sRNAseq", "GSM1376625", null, "source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain", "Female Brain 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 Friedl\u00e4nder 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 m r 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.", "Female Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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.", "gender:Female|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376625", "GSM1376625: Female Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376625", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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:GSM1376625", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB012_CTTGTA_L007_R1.fastq.gz", "fastq", 657620928.0, 12894528.0, "GSM1376625 r1", "0:51", "A:127428594;C:157315630;G:203096060;T:169719399;N:61245", 51, null, null, null, 127428594, 157315630, 203096060, 169719399, 61245, "SRX529137", "SRS598834", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01165, null, 0.00109, null, 0.99622, null, 0.72322, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38015, "SRR1265741", "SRX529136", "SRS598833", "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.", null, "pubmed:26574018", null, "Female Brain Replicate 2 sRNAseq", "GSM1376624", null, "source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain", "Female Brain 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 Friedl\u00e4nder 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 m r 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.", "Female Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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.", "gender:Female|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376624", "GSM1376624: Female Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376624", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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:GSM1376624", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB011_GGCTAC_L007_R1.fastq.gz", "fastq", 197790903.0, 3878253.0, "GSM1376624 r1", "0:51", "A:39219508;C:48781853;G:60339090;T:49430999;N:19453", 51, null, null, null, 39219508, 48781853, 60339090, 49430999, 19453, "SRX529136", "SRS598833", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00227, null, 0.00019, null, 0.99835, null, 0.67164, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38016, "SRR1265740", "SRX529135", "SRS598832", "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.", null, "pubmed:26574018", null, "Female Brain Replicate 1 sRNAseq", "GSM1376623", null, "source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain", "Female Brain 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 Friedl\u00e4nder 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 m r 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.", "Female Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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.", "gender:Female|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376623", "GSM1376623: Female Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376623", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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:GSM1376623", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB010_TAGCTT_L007_R1.fastq.gz", "fastq", 127765710.0, 2505210.0, "GSM1376623 r1", "0:51", "A:24845648;C:31103830;G:38874684;T:32929436;N:12112", 51, null, null, null, 24845648, 31103830, 38874684, 32929436, 12112, "SRX529135", "SRS598832", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.02647, null, 0.00307, null, 0.99368, null, 0.59472, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38017, "SRR1265739", "SRX529134", "SRS598831", "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.", null, "pubmed:26574018", null, "Male Brain Replicate 3 sRNAseq", "GSM1376622", null, "source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain", "Male Brain 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 Friedl\u00e4nder 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 m r 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.", "Male Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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.", "gender:Male|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376622", "GSM1376622: Male Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376622", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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:GSM1376622", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB009_TTAGGC_L007_R1.fastq.gz", "fastq", 749856876.0, 14703076.0, "GSM1376622 r1", "0:51", "A:142133111;C:197021938;G:231006890;T:179625504;N:69433", 51, null, null, null, 142133111, 197021938, 231006890, 179625504, 69433, "SRX529134", "SRS598831", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00196, null, 0.00026, null, 0.99843, null, 0.64615, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38018, "SRR1265738", "SRX529133", "SRS598830", "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.", null, "pubmed:26574018", null, "Male Brain Replicate 2 sRNAseq", "GSM1376621", null, "source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain", "Male Brain 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 Friedl\u00e4nder 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 m r 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.", "Male Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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.", "gender:Male|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376621", "GSM1376621: Male Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376621", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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:GSM1376621", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB008_CGATGT_L007_R1.fastq.gz", "fastq", 394620558.0, 7737658.0, "GSM1376621 r1", "0:51", "A:68213140;C:110690478;G:127130285;T:88550429;N:36226", 51, null, null, null, 68213140, 110690478, 127130285, 88550429, 36226, "SRX529133", "SRS598830", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.06427, null, 0.00768, null, 0.98859, null, 0.77971, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38019, "SRR1265737", "SRX529132", "SRS598829", "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.", null, "pubmed:26574018", null, "Male Brain Replicate 1 sRNAseq", "GSM1376620", null, "source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain", "Male Brain 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 Friedl\u00e4nder 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 m r 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.", "Male Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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.", "gender:Male|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376620", "GSM1376620: Male Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376620", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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:GSM1376620", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB007_ATCACG_L007_R1.fastq.gz", "fastq", 329742489.0, 6465539.0, "GSM1376620 r1", "0:51", "A:60032454;C:91021987;G:104188224;T:74471433;N:28391", 51, null, null, null, 60032454, 91021987, 104188224, 74471433, 28391, "SRX529132", "SRS598829", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00994, null, 0.00098, null, 0.99738, null, 0.77713, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [39614, "SRR1873566", "SRX915246", "SRS870228", "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.", null, "pubmed:26694924", null, "brain", "GSM1630510", null, "source name:adult brain 1 year old|strain/background:AB|genotype/variation:wild type|tissue:brain|developmental stage:adult|age:1 year", "brain", "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 brain 1 year old", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC on a 14 h light/10 h dark cycle.", "strain/background:AB|genotype/variation:wild type|tissue:brain|developmental stage:adult|age:1 year", "GSM1630510", "GSM1630510: brain; Danio rerio; miRNA Seq", "GSM1630510", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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:GSM1630510", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "LS454", "454 GS FLX", null, "SRP056014", null, null, null, null, 688279.0, 12620.0, "GSM1630510 r1", "0:4 1:50.54", "A:205782;C:180028;G:171745;T:129693;N:1031", 4, 50, null, null, 205782, 180028, 171745, 129693, 1031, "SRX915246", "SRS870228", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 48, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "Portugal", "2015-03-09", "Adult", "Adult", "Brain", "Nervous System"], [48625, "SRR7280652", "SRX4184230", "SRS3395609", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, null, "Telencephalon", "Brain Telenc", null, "strain:AB|age:adult|sex:pooled male and female|tissue:Telencephalon|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: telencephalon", "Brain Telenc", "Brain Telenc", "RNA from dissociated telencephalons of males and females", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Brain_Telenc_R1-125.fq.gz Brain_Telenc_R2-125.fq.gz", "fastq fastq", 71366993000.0, 285467972.0, "Brain Telenc R1 125.fq.gz", "0:125 1:125", "A:19965884492;C:15794543428;G:15865015134;T:19703234174;N:38315772", 125, 125, null, null, 19965884492, 15794543428, 15865015134, 19703234174, 38315772, "SRX4184230", "SRS3395609", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.94146, 0.94273, 0.14194, 0.14162, 0.70167, 0.70396, 0.52125, 0.51616, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Adult", "Adult", "Brain", "Nervous System"], [48626, "SRR7280653", "SRX4184229", "SRS3395610", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, null, "Cerebellum", "Cerebellum", null, "strain:AB|age:adult|sex:pooled male and female|tissue:Cerebellum|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: cerebellum", "Cerebellum", "Cerebellum", "RNA from dissociated cerebellum from males and females", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Cerebellum_R1-125.fq.gz Cerebellum_R2-125.fq.gz", "fastq fastq", 34135866750.0, 136543467.0, "Cerebellum R2 125.fq.gz", "0:125 1:125", "A:9659073468;C:7434102293;G:7478952142;T:9549216912;N:14521935", 125, 125, null, null, 9659073468, 7434102293, 7478952142, 9549216912, 14521935, "SRX4184229", "SRS3395610", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.93517, 0.93417, 0.16496, 0.16457, 0.73695, 0.73476, 0.47363, 0.48287, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Adult", "Adult", "Brain", "Nervous System"], [48990, "SRR7612999", "SRX4477699", "SRS3602899", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 156 ZF brain smallRNAseq", "GSM3309607", null, "source name:brain|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "NH FLI 156 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "GSM3309607", "GSM3309607: NH FLI 156 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309607", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309607", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 681376400.0, 13627528.0, "GSM3309607 r1", "0:50", "A:149742268;C:163827889;G:200725169;T:167045618;N:35456", 50, null, null, null, 149742268, 163827889, 200725169, 167045618, 35456, "SRX4477699", "SRS3602899", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.00576, null, 0.00087, null, 0.9959, null, 0.70299, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48991, "SRR7612998", "SRX4477698", "SRS3602898", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 154 ZF brain smallRNAseq", "GSM3309606", null, "source name:brain|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "NH FLI 154 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "GSM3309606", "GSM3309606: NH FLI 154 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309606", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309606", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1196666100.0, 23933322.0, "GSM3309606 r1", "0:50", "A:243243770;C:320296221;G:371488432;T:261584801;N:52876", 50, null, null, null, 243243770, 320296221, 371488432, 261584801, 52876, "SRX4477698", "SRS3602898", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01627, null, 0.00325, null, 0.99293, null, 0.7183, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48992, "SRR7612997", "SRX4477697", "SRS3602897", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 153 ZF brain smallRNAseq", "GSM3309605", null, "source name:brain|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "NH FLI 153 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "GSM3309605", "GSM3309605: NH FLI 153 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309605", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309605", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 2123002650.0, 42460053.0, "GSM3309605 r1", "0:50", "A:461619025;C:513713514;G:623358074;T:524212056;N:99981", 50, null, null, null, 461619025, 513713514, 623358074, 524212056, 99981, "SRX4477697", "SRS3602897", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02759, null, 0.00329, null, 0.99287, null, 0.62418, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48993, "SRR7612996", "SRX4477696", "SRS3602896", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 152 ZF brain smallRNAseq", "GSM3309604", null, "source name:brain|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "NH FLI 152 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "GSM3309604", "GSM3309604: NH FLI 152 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309604", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309604", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1434455750.0, 28689115.0, "GSM3309604 r1", "0:50", "A:283488481;C:381046485;G:446805516;T:323062667;N:52601", 50, null, null, null, 283488481, 381046485, 446805516, 323062667, 52601, "SRX4477696", "SRS3602896", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.04109, null, 0.00889, null, 0.98786, null, 0.73333, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48994, "SRR7612995", "SRX4477695", "SRS3602895", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 150 ZF brain smallRNAseq", "GSM3309603", null, "source name:brain|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "NH FLI 150 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male", "GSM3309603", "GSM3309603: NH FLI 150 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309603", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309603", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1338770950.0, 26775419.0, "GSM3309603 r1", "0:50", "A:269497925;C:353627074;G:405585207;T:310020028;N:40716", 50, null, null, null, 269497925, 353627074, 405585207, 310020028, 40716, "SRX4477695", "SRS3602895", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02887, null, 0.00518, null, 0.99052, null, 0.68568, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48995, "SRR7612994", "SRX4477694", "SRS3602894", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 143 ZF brain smallRNAseq", "GSM3309602", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "NH FLI 143 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "GSM3309602", "GSM3309602: NH FLI 143 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309602", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309602", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 626017200.0, 12520344.0, "GSM3309602 r1", "0:50", "A:134906441;C:152023722;G:185947594;T:153106683;N:32760", 50, null, null, null, 134906441, 152023722, 185947594, 153106683, 32760, "SRX4477694", "SRS3602894", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.00695, null, 0.00127, null, 0.99529, null, 0.71945, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48996, "SRR7612993", "SRX4477693", "SRS3602893", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 142 ZF brain smallRNAseq", "GSM3309601", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "NH FLI 142 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "GSM3309601", "GSM3309601: NH FLI 142 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309601", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309601", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 602153350.0, 12043067.0, "GSM3309601 r1", "0:50", "A:130038217;C:144346274;G:180485776;T:147255994;N:27089", 50, null, null, null, 130038217, 144346274, 180485776, 147255994, 27089, "SRX4477693", "SRS3602893", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01383, null, 0.002, null, 0.99545, null, 0.61426, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48997, "SRR7612992", "SRX4477692", "SRS3602892", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 140 ZF brain smallRNAseq", "GSM3309600", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "NH FLI 140 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "GSM3309600", "GSM3309600: NH FLI 140 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309600", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309600", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1040923600.0, 20818472.0, "GSM3309600 r1", "0:50", "A:226013762;C:247845507;G:308453469;T:258569100;N:41762", 50, null, null, null, 226013762, 247845507, 308453469, 258569100, 41762, "SRX4477692", "SRS3602892", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01433, null, 0.00292, null, 0.99484, null, 0.60865, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48998, "SRR7612991", "SRX4477691", "SRS3602891", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 139 ZF brain smallRNAseq", "GSM3309599", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "NH FLI 139 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "GSM3309599", "GSM3309599: NH FLI 139 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309599", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309599", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 612192100.0, 12243842.0, "GSM3309599 r1", "0:50", "A:133152501;C:147001376;G:181291514;T:150727221;N:19488", 50, null, null, null, 133152501, 147001376, 181291514, 150727221, 19488, "SRX4477691", "SRS3602891", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01776, null, 0.00244, null, 0.9945, null, 0.59354, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [48999, "SRR7612990", "SRX4477690", "SRS3602890", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 138 ZF brain smallRNAseq", "GSM3309598", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "NH FLI 138 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:2 years|Sex:male", "GSM3309598", "GSM3309598: NH FLI 138 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309598", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309598", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1205010900.0, 24100218.0, "GSM3309598 r1", "0:50", "A:254443623;C:292846390;G:362958072;T:294704148;N:58667", 50, null, null, null, 254443623, 292846390, 362958072, 294704148, 58667, "SRX4477690", "SRS3602890", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02329, null, 0.00277, null, 0.99442, null, 0.57362, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49000, "SRR7612989", "SRX4477689", "SRS3602889", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 129 ZF brain smallRNAseq", "GSM3309597", null, "source name:brain|strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "NH FLI 129 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "GSM3309597", "GSM3309597: NH FLI 129 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309597", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309597", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 905166650.0, 18103333.0, "GSM3309597 r1", "0:50", "A:183798257;C:231083843;G:277164667;T:213076607;N:43276", 50, null, null, null, 183798257, 231083843, 277164667, 213076607, 43276, "SRX4477689", "SRS3602889", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.03359, null, 0.00484, null, 0.99105, null, 0.62836, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49001, "SRR7612988", "SRX4477688", "SRS3602888", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 128 ZF brain smallRNAseq", "GSM3309596", null, "source name:brain|strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "NH FLI 128 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "GSM3309596", "GSM3309596: NH FLI 128 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309596", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309596", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1304729150.0, 26094583.0, "GSM3309596 r1", "0:50", "A:261793442;C:350134689;G:395019822;T:297741148;N:40049", 50, null, null, null, 261793442, 350134689, 395019822, 297741148, 40049, "SRX4477688", "SRS3602888", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02649, null, 0.00457, null, 0.99038, null, 0.65849, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49002, "SRR7612987", "SRX4477687", "SRS3602887", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 127 ZF brain smallRNAseq", "GSM3309595", null, "source name:brain|strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "NH FLI 127 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "GSM3309595", "GSM3309595: NH FLI 127 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309595", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309595", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1087717850.0, 21754357.0, "GSM3309595 r1", "0:50", "A:233191242;C:266842531;G:322704369;T:264927170;N:52538", 50, null, null, null, 233191242, 266842531, 322704369, 264927170, 52538, "SRX4477687", "SRS3602887", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02888, null, 0.00371, null, 0.99322, null, 0.60352, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49003, "SRR7612986", "SRX4477686", "SRS3602886", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 125 ZF brain smallRNAseq", "GSM3309594", null, "source name:brain|strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "NH FLI 125 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "GSM3309594", "GSM3309594: NH FLI 125 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309594", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309594", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 745015250.0, 14900305.0, "GSM3309594 r1", "0:50", "A:160725228;C:177900490;G:219158125;T:187195853;N:35554", 50, null, null, null, 160725228, 177900490, 219158125, 187195853, 35554, "SRX4477686", "SRS3602886", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02669, null, 0.00263, null, 0.99348, null, 0.564, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49004, "SRR7612985", "SRX4477685", "SRS3602885", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 124 ZF brain smallRNAseq", "GSM3309593", null, "source name:brain|strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "NH FLI 124 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male", "GSM3309593", "GSM3309593: NH FLI 124 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309593", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309593", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1305373550.0, 26107471.0, "GSM3309593 r1", "0:50", "A:303613747;C:302726844;G:364736102;T:334233710;N:63147", 50, null, null, null, 303613747, 302726844, 364736102, 334233710, 63147, "SRX4477685", "SRS3602885", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.03499, null, 0.00371, null, 0.99362, null, 0.5891, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49005, "SRR7612984", "SRX4477684", "SRS3602884", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 114 ZF brain smallRNAseq", "GSM3309592", null, "source name:brain|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "NH FLI 114 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "GSM3309592", "GSM3309592: NH FLI 114 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309592", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309592", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 722165700.0, 14443314.0, "GSM3309592 r1", "0:50", "A:158514262;C:171787722;G:214687494;T:177143548;N:32674", 50, null, null, null, 158514262, 171787722, 214687494, 177143548, 32674, "SRX4477684", "SRS3602884", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01251, null, 0.00195, null, 0.99584, null, 0.60892, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49006, "SRR7612983", "SRX4477683", "SRS3602883", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 109 ZF brain smallRNAseq", "GSM3309591", null, "source name:brain|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "NH FLI 109 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "GSM3309591", "GSM3309591: NH FLI 109 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309591", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309591", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1295539450.0, 25910789.0, "GSM3309591 r1", "0:50", "A:292712777;C:309650541;G:373811139;T:319271810;N:93183", 50, null, null, null, 292712777, 309650541, 373811139, 319271810, 93183, "SRX4477683", "SRS3602883", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.07779, null, 0.00531, null, 0.99431, null, 0.5455, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49007, "SRR7612982", "SRX4477682", "SRS3602882", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 99 100 ZF brain smallRNAseq", "GSM3309590", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "NH FLI 99 100 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "GSM3309590", "GSM3309590: NH FLI 99 100 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309590", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309590", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 433373950.0, 8667479.0, "GSM3309590 r1", "0:50", "A:93001141;C:105441767;G:129717150;T:105194380;N:19512", 50, null, null, null, 93001141, 105441767, 129717150, 105194380, 19512, "SRX4477682", "SRS3602882", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01476, null, 0.0021, null, 0.99555, null, 0.64442, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49008, "SRR7612981", "SRX4477681", "SRS3602881", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 97 98 ZF brain smallRNAseq", "GSM3309589", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "NH FLI 97 98 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "GSM3309589", "GSM3309589: NH FLI 97 98 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309589", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309589", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 510617150.0, 10212343.0, "GSM3309589 r1", "0:50", "A:110447838;C:121736402;G:152183388;T:126228958;N:20564", 50, null, null, null, 110447838, 121736402, 152183388, 126228958, 20564, "SRX4477681", "SRS3602881", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01519, null, 0.00277, null, 0.99409, null, 0.63157, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49009, "SRR7612980", "SRX4477680", "SRS3602880", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 95 96 ZF brain smallRNAseq", "GSM3309588", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "NH FLI 95 96 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "GSM3309588", "GSM3309588: NH FLI 95 96 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309588", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309588", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 472516100.0, 9450322.0, "GSM3309588 r1", "0:50", "A:103765011;C:113400404;G:139267589;T:116067916;N:15180", 50, null, null, null, 103765011, 113400404, 139267589, 116067916, 15180, "SRX4477680", "SRS3602880", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01894, null, 0.00292, null, 0.99411, null, 0.58808, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49010, "SRR7612979", "SRX4477679", "SRS3602879", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 116 ZF brain smallRNAseq", "GSM3309587", null, "source name:brain|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "NH FLI 116 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "GSM3309587", "GSM3309587: NH FLI 116 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309587", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309587", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 715226800.0, 14304536.0, "GSM3309587 r1", "0:50", "A:159838696;C:168777427;G:208871390;T:177701320;N:37967", 50, null, null, null, 159838696, 168777427, 208871390, 177701320, 37967, "SRX4477679", "SRS3602879", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.00535, null, 0.00095, null, 0.99677, null, 0.70896, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49011, "SRR7612978", "SRX4477678", "SRS3602878", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 112 ZF brain smallRNAseq", "GSM3309586", null, "source name:brain|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "NH FLI 112 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "GSM3309586", "GSM3309586: NH FLI 112 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309586", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309586", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1026870700.0, 20537414.0, "GSM3309586 r1", "0:50", "A:221725135;C:249408204;G:304663061;T:251034143;N:40157", 50, null, null, null, 221725135, 249408204, 304663061, 251034143, 40157, "SRX4477678", "SRS3602878", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01708, null, 0.00331, null, 0.99354, null, 0.66357, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49012, "SRR7612977", "SRX4477677", "SRS3602877", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 111 ZF brain smallRNAseq", "GSM3309585", null, "source name:brain|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "NH FLI 111 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male", "GSM3309585", "GSM3309585: NH FLI 111 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309585", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309585", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 743568750.0, 14871375.0, "GSM3309585 r1", "0:50", "A:166161134;C:175989827;G:216120925;T:185273082;N:23782", 50, null, null, null, 166161134, 175989827, 216120925, 185273082, 23782, "SRX4477677", "SRS3602877", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01548, null, 0.00239, null, 0.99515, null, 0.60786, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49013, "SRR7612976", "SRX4477676", "SRS3602906", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 103 104 ZF brain smallRNAseq", "GSM3309584", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "NH FLI 103 104 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "GSM3309584", "GSM3309584: NH FLI 103 104 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309584", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309584", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 1106423150.0, 22128463.0, "GSM3309584 r1", "0:50", "A:234017026;C:276221869;G:334967256;T:261138362;N:78637", 50, null, null, null, 234017026, 276221869, 334967256, 261138362, 78637, "SRX4477676", "SRS3602906", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.07804, null, 0.00455, null, 0.99263, null, 0.55094, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [49014, "SRR7612975", "SRX4477675", "SRS3602876", "SRP155545", "PRJNA483217", "Sequencing of Danio rerio brain for 5 age groups", "GSE117807", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.", null, null, null, "NH FLI 101 102 ZF brain smallRNAseq", "GSM3309583", null, "source name:brain|strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "NH FLI 101 102 ZF brain smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "brain", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:brain|age:6 month|Sex:male", "GSM3309583", "GSM3309583: NH FLI 101 102 ZF brain smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309583", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309583", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155545", null, null, null, null, 929857100.0, 18597142.0, "GSM3309583 r1", "0:50", "A:195349293;C:237069996;G:279453097;T:217936195;N:48519", 50, null, null, null, 195349293, 237069996, 279453097, 217936195, 48519, "SRX4477675", "SRS3602876", "SRA745937", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01233, null, 0.00233, null, 0.99417, null, 0.76993, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Brain", "Nervous System"], [67823, "SRR17335719", "SRX13511115", "SRS11405356", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF3", "GSM5754470", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754470", "GSM5754470: CPF3; Danio rerio; ncRNA Seq", "GSM5754470 r1", "GSM5754470", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF3_1.fq.gz CPF3_2.fq.gz", "fastq fastq", 12726241500.0, 42420805.0, "GSM5754470 r1", "0:150 1:150", "A:3447613023;C:2896153797;G:2922038320;T:3459698412;N:737948", 150, 150, null, null, 3447613023, 2896153797, 2922038320, 3459698412, 737948, "SRX13511115", "SRS11405356", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89399, 0.89612, 0.38172, 0.37657, 0.66628, 0.66799, 0.53056, 0.53213, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67824, "SRR17335720", "SRX13511114", "SRS11405355", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF2", "GSM5754469", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754469", "GSM5754469: CPF2; Danio rerio; ncRNA Seq", "GSM5754469 r1", "GSM5754469", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF2_1.fq.gz CPF2_2.fq.gz", "fastq fastq", 14881715100.0, 49605717.0, "GSM5754469 r1", "0:150 1:150", "A:4214905088;C:3201163283;G:3225795074;T:4239665352;N:186303", 150, 150, null, null, 4214905088, 3201163283, 3225795074, 4239665352, 186303, "SRX13511114", "SRS11405355", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87491, 0.87638, 0.40844, 0.40479, 0.67123, 0.67018, 0.49174, 0.48952, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67825, "SRR17335721", "SRX13511113", "SRS11405354", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF1", "GSM5754468", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754468", "GSM5754468: CPF1; Danio rerio; ncRNA Seq", "GSM5754468 r1", "GSM5754468", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF1_1.fq.gz CPF1_2.fq.gz", "fastq fastq", 16447798800.0, 54825996.0, "GSM5754468 r1", "0:150 1:150", "A:4454573413;C:3748270411;G:3776995203;T:4467442717;N:517056", 150, 150, null, null, 4454573413, 3748270411, 3776995203, 4467442717, 517056, "SRX13511113", "SRS11405354", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89313, 0.8947, 0.35381, 0.35194, 0.64954, 0.64831, 0.51962, 0.52475, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67826, "SRR17335722", "SRX13511112", "SRS11405353", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP3", "GSM5754467", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754467", "GSM5754467: CYP3; Danio rerio; ncRNA Seq", "GSM5754467 r1", "GSM5754467", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP3_1.fq.gz CYP3_2.fq.gz", "fastq fastq", 13417868100.0, 44726227.0, "GSM5754467 r1", "0:150 1:150", "A:3645134270;C:3041754103;G:3084809543;T:3645750889;N:419295", 150, 150, null, null, 3645134270, 3041754103, 3084809543, 3645750889, 419295, "SRX13511112", "SRS11405353", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86122, 0.8638, 0.4112, 0.40785, 0.68738, 0.68519, 0.54768, 0.44856, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67827, "SRR17335723", "SRX13511111", "SRS11405352", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP2", "GSM5754466", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754466", "GSM5754466: CYP2; Danio rerio; ncRNA Seq", "GSM5754466 r1", "GSM5754466", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP2_1.fq.gz CYP2_2.fq.gz", "fastq fastq", 13096007700.0, 43653359.0, "GSM5754466 r1", "0:150 1:150", "A:3638241155;C:2892284693;G:2925857490;T:3639296449;N:327913", 150, 150, null, null, 3638241155, 2892284693, 2925857490, 3639296449, 327913, "SRX13511111", "SRS11405352", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85953, 0.86247, 0.41975, 0.41734, 0.68174, 0.67862, 0.52504, 0.5324, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67828, "SRR17335724", "SRX13511110", "SRS11405351", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP1", "GSM5754465", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754465", "GSM5754465: CYP1; Danio rerio; ncRNA Seq", "GSM5754465 r1", "GSM5754465", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP1_1.fq.gz CYP1_2.fq.gz", "fastq fastq", 16372872000.0, 54576240.0, "GSM5754465 r1", "0:150 1:150", "A:4747286217;C:3417115980;G:3453793026;T:4754530080;N:146697", 150, 150, null, null, 4747286217, 3417115980, 3453793026, 4754530080, 146697, "SRX13511110", "SRS11405351", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85322, 0.85414, 0.46298, 0.45901, 0.68016, 0.67866, 0.47694, 0.47897, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67829, "SRR17335725", "SRX13511109", "SRS11405350", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont3", "GSM5754464", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754464", "GSM5754464: Cont3; Danio rerio; ncRNA Seq", "GSM5754464 r1", "GSM5754464", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont3_1.fq.gz Cont3_2.fq.gz", "fastq fastq", 15202443900.0, 50674813.0, "GSM5754464 r1", "0:150 1:150", "A:4400470018;C:3173803928;G:3218623722;T:4409335756;N:210476", 150, 150, null, null, 4400470018, 3173803928, 3218623722, 4409335756, 210476, "SRX13511109", "SRS11405350", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86129, 0.84677, 0.45657, 0.44799, 0.67884, 0.68083, 0.48291, 0.4763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67830, "SRR17335726", "SRX13511108", "SRS11405349", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont2", "GSM5754463", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754463", "GSM5754463: Cont2; Danio rerio; ncRNA Seq", "GSM5754463 r1", "GSM5754463", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont2_1.fq.gz Cont2_2.fq.gz", "fastq fastq", 12927267600.0, 43090892.0, "GSM5754463 r1", "0:150 1:150", "A:3474574877;C:2959326086;G:3006553706;T:3486600752;N:212179", 150, 150, null, null, 3474574877, 2959326086, 3006553706, 3486600752, 212179, "SRX13511108", "SRS11405349", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87695, 0.87907, 0.41673, 0.41416, 0.69266, 0.69266, 0.53339, 0.58145, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67831, "SRR17335727", "SRX13511107", "SRS11405348", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont1", "GSM5754462", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system such as the cell the organism and the ecosystem from molecular level information especially large scale molecular datasets generated by genome sequencing and other high throughput experimental technologies http://www.genome.jp/kegg/. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754462", "GSM5754462: Cont1; Danio rerio; ncRNA Seq", "GSM5754462 r1", "GSM5754462", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont1_1.fq.gz Cont1_2.fq.gz", "fastq fastq", 18395362500.0, 61317875.0, "GSM5754462 r1", "0:150 1:150", "A:5379624768;C:3792463355;G:3842313235;T:5380702187;N:258955", 150, 150, null, null, 5379624768, 3792463355, 3842313235, 5380702187, 258955, "SRX13511107", "SRS11405348", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.83439, 0.83446, 0.45703, 0.44894, 0.68828, 0.68578, 0.4957, 0.49639, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 47, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_selection\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "size fractionation", "p1": "Brain"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": 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"toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&tissue_curation=Brain", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&tissue_curation=Brain&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&tissue_curation=Brain&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&tissue_curation=Brain", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 46, "toggle_url": 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