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46 rows where experiment.library_selection = "size fractionation", technology = "unknown" and tissue_curation_coarse = "Nervous System"

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experiment.library_strategy 3

devstage_curation_coarse 3

experiment.library_layout 2

devstage_curation 2

tissue_curation_coarse 1

  • Nervous System · 46 ✖

tissue_curation 1

technology 1

  • unknown · 46 ✖

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 46 ✖
Link 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
32926 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.         M2b   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                 midRNA seq Danio rerio 07 07 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     M2b_R1.fq.gz M2b_R2.fq.gz fastq fastq 9324874800.0 31082916.0 M2b R1.fq.gz 0:150 1:150 A:2073617286;C:2382074775;G:2948687855;T:1920389281;N:105603 150 150     2073617286 2382074775 2948687855 1920389281 105603 SRX25008882 SRS21709101 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.57388 0.29571 0.04187 0.10168 0.99506 0.99513 0.61677 0.60641 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Brain Nervous System
32928 32928 SRR29498572 SRX25008880 SRS21709099 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.         M1b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M1b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 05 05 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     M1b_R1.fq.gz M1b_R2.fq.gz fastq fastq 7947472800.0 26491576.0 M1b R1.fq.gz 0:150 1:150 A:1764190500;C:1937842699;G:2595509352;T:1649839967;N:90282 150 150     1764190500 1937842699 2595509352 1649839967 90282 SRX25008880 SRS21709099 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96542 0.21476 0.17288 0.05982 0.97289 0.99711 0.57845 0.611 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Brain Nervous System
32930 32930 SRR29498574 SRX25008878 SRS21709097 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.         F2b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F2b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 03 03 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     F2b_R1.fq.gz F2b_R2.fq.gz fastq fastq 9249410100.0 30831367.0 F2b R1.fq.gz 0:150 1:150 A:2101671138;C:2272479255;G:2931272789;T:1943881150;N:105768 150 150     2101671138 2272479255 2931272789 1943881150 105768 SRX25008878 SRS21709097 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96654 0.19343 0.23127 0.08081 0.95272 0.99326 0.63762 0.64901 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Brain Nervous System
32934 32934 SRR29498578 SRX25008874 SRS21709093 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.         F1b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F1b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 01 01 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     F1b_R2.fq.gz F1b_R1.fq.gz fastq fastq 7995852300.0 26652841.0 F1b R1.fq.gz 0:150 1:150 A:1744452113;C:2053788787;G:2580416325;T:1617104387;N:90688 150 150     1744452113 2053788787 2580416325 1617104387 90688 SRX25008874 SRS21709093 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96107 0.17798 0.16452 0.02921 0.96759 0.99677 0.66455 0.62672 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Brain Nervous System
38014 38014 SRR1265742 SRX529137 SRS598834 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Brain Replicate 3 sRNAseq GSM1376625   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 Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Brain|genetic background:Wild type Singapore strain GSM1376625 GSM1376625: Female Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376625   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376625 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     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       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   0.00109   0.99622   0.72322   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38015 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.   pubmed:26574018   Female Brain Replicate 2 sRNAseq GSM1376624   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 Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Brain|genetic background:Wild type Singapore strain GSM1376624 GSM1376624: Female Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376624   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376624 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     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       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   0.00019   0.99835   0.67164   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38016 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.   pubmed:26574018   Female Brain Replicate 1 sRNAseq GSM1376623   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 Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Brain|genetic background:Wild type Singapore strain GSM1376623 GSM1376623: Female Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376623   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376623 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     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       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   0.00307   0.99368   0.59472   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38017 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.   pubmed:26574018   Male Brain Replicate 3 sRNAseq GSM1376622   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 Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Brain|genetic background:Wild type Singapore strain GSM1376622 GSM1376622: Male Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376622   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376622 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     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       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   0.00026   0.99843   0.64615   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38018 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.   pubmed:26574018   Male Brain Replicate 2 sRNAseq GSM1376621   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 Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Brain|genetic background:Wild type Singapore strain GSM1376621 GSM1376621: Male Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376621   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376621 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     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       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   0.00768   0.98859   0.77971   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
38019 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.   pubmed:26574018   Male Brain Replicate 1 sRNAseq GSM1376620   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 Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Brain N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Brain|genetic background:Wild type Singapore strain GSM1376620 GSM1376620: Male Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376620   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376620 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     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       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   0.00098   0.99738   0.77713   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Brain Nervous System
48625 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       Telencephalon Brain Telenc   strain:AB|age:adult|sex:pooled male and female|tissue:Telencephalon|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: telencephalon Brain Telenc Brain Telenc RNA from dissociated telencephalons of males and females     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     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     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   Spain 2019-01-22 Adult Adult Brain Nervous System
48626 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       Cerebellum Cerebellum   strain:AB|age:adult|sex:pooled male and female|tissue:Cerebellum|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: cerebellum Cerebellum Cerebellum RNA from dissociated cerebellum from males and females     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     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     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   Spain 2019-01-22 Adult Adult Brain Nervous System
48990 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.       NH FLI 156 ZF brain smallRNAseq GSM3309607   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   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.   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   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   SRP155545         681376400.0 13627528.0 GSM3309607 r1 0:50 A:149742268;C:163827889;G:200725169;T:167045618;N:35456 50       149742268 163827889 200725169 167045618 35456 SRX4477699 SRS3602899 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00576   0.00087   0.9959   0.70299   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48991 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.       NH FLI 154 ZF brain smallRNAseq GSM3309606   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   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.   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   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   SRP155545         1196666100.0 23933322.0 GSM3309606 r1 0:50 A:243243770;C:320296221;G:371488432;T:261584801;N:52876 50       243243770 320296221 371488432 261584801 52876 SRX4477698 SRS3602898 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01627   0.00325   0.99293   0.7183   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48992 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.       NH FLI 153 ZF brain smallRNAseq GSM3309605   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   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.   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   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   SRP155545         2123002650.0 42460053.0 GSM3309605 r1 0:50 A:461619025;C:513713514;G:623358074;T:524212056;N:99981 50       461619025 513713514 623358074 524212056 99981 SRX4477697 SRS3602897 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02759   0.00329   0.99287   0.62418   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48993 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.       NH FLI 152 ZF brain smallRNAseq GSM3309604   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   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.   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   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   SRP155545         1434455750.0 28689115.0 GSM3309604 r1 0:50 A:283488481;C:381046485;G:446805516;T:323062667;N:52601 50       283488481 381046485 446805516 323062667 52601 SRX4477696 SRS3602896 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.04109   0.00889   0.98786   0.73333   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48994 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.       NH FLI 150 ZF brain smallRNAseq GSM3309603   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   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.   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   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   SRP155545         1338770950.0 26775419.0 GSM3309603 r1 0:50 A:269497925;C:353627074;G:405585207;T:310020028;N:40716 50       269497925 353627074 405585207 310020028 40716 SRX4477695 SRS3602895 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02887   0.00518   0.99052   0.68568   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48995 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.       NH FLI 143 ZF brain smallRNAseq GSM3309602   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   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.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309602 GSM3309602: NH FLI 143 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309602   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   SRP155545         626017200.0 12520344.0 GSM3309602 r1 0:50 A:134906441;C:152023722;G:185947594;T:153106683;N:32760 50       134906441 152023722 185947594 153106683 32760 SRX4477694 SRS3602894 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00695   0.00127   0.99529   0.71945   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48996 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.       NH FLI 142 ZF brain smallRNAseq GSM3309601   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   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.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309601 GSM3309601: NH FLI 142 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309601   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   SRP155545         602153350.0 12043067.0 GSM3309601 r1 0:50 A:130038217;C:144346274;G:180485776;T:147255994;N:27089 50       130038217 144346274 180485776 147255994 27089 SRX4477693 SRS3602893 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01383   0.002   0.99545   0.61426   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48997 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.       NH FLI 140 ZF brain smallRNAseq GSM3309600   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   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.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309600 GSM3309600: NH FLI 140 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309600   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   SRP155545         1040923600.0 20818472.0 GSM3309600 r1 0:50 A:226013762;C:247845507;G:308453469;T:258569100;N:41762 50       226013762 247845507 308453469 258569100 41762 SRX4477692 SRS3602892 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01433   0.00292   0.99484   0.60865   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48998 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.       NH FLI 139 ZF brain smallRNAseq GSM3309599   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   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.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309599 GSM3309599: NH FLI 139 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309599   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   SRP155545         612192100.0 12243842.0 GSM3309599 r1 0:50 A:133152501;C:147001376;G:181291514;T:150727221;N:19488 50       133152501 147001376 181291514 150727221 19488 SRX4477691 SRS3602891 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01776   0.00244   0.9945   0.59354   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48999 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.       NH FLI 138 ZF brain smallRNAseq GSM3309598   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   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.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309598 GSM3309598: NH FLI 138 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309598   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   SRP155545         1205010900.0 24100218.0 GSM3309598 r1 0:50 A:254443623;C:292846390;G:362958072;T:294704148;N:58667 50       254443623 292846390 362958072 294704148 58667 SRX4477690 SRS3602890 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02329   0.00277   0.99442   0.57362   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49000 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.       NH FLI 129 ZF brain smallRNAseq GSM3309597   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   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.   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   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   SRP155545         905166650.0 18103333.0 GSM3309597 r1 0:50 A:183798257;C:231083843;G:277164667;T:213076607;N:43276 50       183798257 231083843 277164667 213076607 43276 SRX4477689 SRS3602889 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03359   0.00484   0.99105   0.62836   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49001 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.       NH FLI 128 ZF brain smallRNAseq GSM3309596   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   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.   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   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   SRP155545         1304729150.0 26094583.0 GSM3309596 r1 0:50 A:261793442;C:350134689;G:395019822;T:297741148;N:40049 50       261793442 350134689 395019822 297741148 40049 SRX4477688 SRS3602888 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02649   0.00457   0.99038   0.65849   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49002 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.       NH FLI 127 ZF brain smallRNAseq GSM3309595   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   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.   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   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   SRP155545         1087717850.0 21754357.0 GSM3309595 r1 0:50 A:233191242;C:266842531;G:322704369;T:264927170;N:52538 50       233191242 266842531 322704369 264927170 52538 SRX4477687 SRS3602887 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02888   0.00371   0.99322   0.60352   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49003 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.       NH FLI 125 ZF brain smallRNAseq GSM3309594   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   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.   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   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   SRP155545         745015250.0 14900305.0 GSM3309594 r1 0:50 A:160725228;C:177900490;G:219158125;T:187195853;N:35554 50       160725228 177900490 219158125 187195853 35554 SRX4477686 SRS3602886 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02669   0.00263   0.99348   0.564   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49004 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.       NH FLI 124 ZF brain smallRNAseq GSM3309593   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   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.   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   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   SRP155545         1305373550.0 26107471.0 GSM3309593 r1 0:50 A:303613747;C:302726844;G:364736102;T:334233710;N:63147 50       303613747 302726844 364736102 334233710 63147 SRX4477685 SRS3602885 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03499   0.00371   0.99362   0.5891   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49005 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.       NH FLI 114 ZF brain smallRNAseq GSM3309592   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   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.   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   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   SRP155545         722165700.0 14443314.0 GSM3309592 r1 0:50 A:158514262;C:171787722;G:214687494;T:177143548;N:32674 50       158514262 171787722 214687494 177143548 32674 SRX4477684 SRS3602884 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01251   0.00195   0.99584   0.60892   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49006 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.       NH FLI 109 ZF brain smallRNAseq GSM3309591   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   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.   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   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   SRP155545         1295539450.0 25910789.0 GSM3309591 r1 0:50 A:292712777;C:309650541;G:373811139;T:319271810;N:93183 50       292712777 309650541 373811139 319271810 93183 SRX4477683 SRS3602883 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.07779   0.00531   0.99431   0.5455   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49007 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.       NH FLI 99 100 ZF brain smallRNAseq GSM3309590   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   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.   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   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   SRP155545         433373950.0 8667479.0 GSM3309590 r1 0:50 A:93001141;C:105441767;G:129717150;T:105194380;N:19512 50       93001141 105441767 129717150 105194380 19512 SRX4477682 SRS3602882 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01476   0.0021   0.99555   0.64442   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49008 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.       NH FLI 97 98 ZF brain smallRNAseq GSM3309589   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   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.   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   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   SRP155545         510617150.0 10212343.0 GSM3309589 r1 0:50 A:110447838;C:121736402;G:152183388;T:126228958;N:20564 50       110447838 121736402 152183388 126228958 20564 SRX4477681 SRS3602881 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01519   0.00277   0.99409   0.63157   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49009 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.       NH FLI 95 96 ZF brain smallRNAseq GSM3309588   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   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.   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   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   SRP155545         472516100.0 9450322.0 GSM3309588 r1 0:50 A:103765011;C:113400404;G:139267589;T:116067916;N:15180 50       103765011 113400404 139267589 116067916 15180 SRX4477680 SRS3602880 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01894   0.00292   0.99411   0.58808   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49010 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.       NH FLI 116 ZF brain smallRNAseq GSM3309587   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   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.   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   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   SRP155545         715226800.0 14304536.0 GSM3309587 r1 0:50 A:159838696;C:168777427;G:208871390;T:177701320;N:37967 50       159838696 168777427 208871390 177701320 37967 SRX4477679 SRS3602879 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00535   0.00095   0.99677   0.70896   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49011 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.       NH FLI 112 ZF brain smallRNAseq GSM3309586   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   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.   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   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   SRP155545         1026870700.0 20537414.0 GSM3309586 r1 0:50 A:221725135;C:249408204;G:304663061;T:251034143;N:40157 50       221725135 249408204 304663061 251034143 40157 SRX4477678 SRS3602878 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01708   0.00331   0.99354   0.66357   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49012 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.       NH FLI 111 ZF brain smallRNAseq GSM3309585   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   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.   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   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   SRP155545         743568750.0 14871375.0 GSM3309585 r1 0:50 A:166161134;C:175989827;G:216120925;T:185273082;N:23782 50       166161134 175989827 216120925 185273082 23782 SRX4477677 SRS3602877 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01548   0.00239   0.99515   0.60786   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49013 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.       NH FLI 103 104 ZF brain smallRNAseq GSM3309584   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   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.   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   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   SRP155545         1106423150.0 22128463.0 GSM3309584 r1 0:50 A:234017026;C:276221869;G:334967256;T:261138362;N:78637 50       234017026 276221869 334967256 261138362 78637 SRX4477676 SRS3602906 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.07804   0.00455   0.99263   0.55094   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49014 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.       NH FLI 101 102 ZF brain smallRNAseq GSM3309583   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   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.   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   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   SRP155545         929857100.0 18597142.0 GSM3309583 r1 0:50 A:195349293;C:237069996;G:279453097;T:217936195;N:48519 50       195349293 237069996 279453097 217936195 48519 SRX4477675 SRS3602876 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01233   0.00233   0.99417   0.76993   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
67823 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   pubmed:35304207   CPF3 GSM5754470   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     3447613023 2896153797 2922038320 3459698412 737948 SRX13511115 SRS11405356 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67824 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   pubmed:35304207   CPF2 GSM5754469   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     4214905088 3201163283 3225795074 4239665352 186303 SRX13511114 SRS11405355 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67825 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   pubmed:35304207   CPF1 GSM5754468   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     4454573413 3748270411 3776995203 4467442717 517056 SRX13511113 SRS11405354 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67826 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   pubmed:35304207   CYP3 GSM5754467   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     3645134270 3041754103 3084809543 3645750889 419295 SRX13511112 SRS11405353 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67827 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   pubmed:35304207   CYP2 GSM5754466   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     3638241155 2892284693 2925857490 3639296449 327913 SRX13511111 SRS11405352 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67828 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   pubmed:35304207   CYP1 GSM5754465   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     4747286217 3417115980 3453793026 4754530080 146697 SRX13511110 SRS11405351 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67829 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   pubmed:35304207   Cont3 GSM5754464   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     4400470018 3173803928 3218623722 4409335756 210476 SRX13511109 SRS11405350 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67830 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   pubmed:35304207   Cont2 GSM5754463   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     3474574877 2959326086 3006553706 3486600752 212179 SRX13511108 SRS11405349 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System
67831 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   pubmed:35304207   Cont1 GSM5754462   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–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon 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’s 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 … Brain tissue   Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols   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   ncRNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 4000   SRP352585   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     5379624768 3792463355 3842313235 5380702187 258955 SRX13511107 SRS11405348 SRA1349262 Atatürk University Atatürk 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   Turkey 2021-12-27 Undetermined Undetermined Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;