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
37923,SRR1554489,SRX685394,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP039502,,,ZF2_Heart_3.fq.gz,fastq,1302765670.0,12898670.0,Heart2 Run3,0:101,A:397689061;C:312745449;G:268626802;T:323141419;N:562939,101,,,,397689061,312745449,268626802,323141419,562939,SRX685394,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37927,SRR1554477,SRX685389,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP039502,,,ZF1_Heart_3.fq.gz,fastq,1561371524.0,15459124.0,Heart1 Run3,0:101,A:454757966;C:391143691;G:334715236;T:380114024;N:640607,101,,,,454757966,391143691,334715236,380114024,640607,SRX685389,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37933,SRR1554487,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,510Application ReadForward1,SRP039502,,,ZF2_Heart_1.fq.gz,fastq,767836212.0,15055612.0,Heart2 Run1,0:51,A:192620363;C:202013249;G:191038597;T:181862075;N:301928,51,,,,192620363,202013249,191038597,181862075,301928,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,3e-05,,0.99995,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37934,SRR1554488,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,510Application ReadForward1,SRP039502,,,ZF2_Heart_2.fq.gz,fastq,979886205.0,19213455.0,Heart2 Run2,0:51,A:246169086;C:264387065;G:236377487;T:227289693;N:5662874,51,,,,246169086,264387065,236377487,227289693,5662874,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37941,SRR1554475,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,510Application ReadForward1,SRP039502,,,ZF1_Heart_1.fq.gz,fastq,810162642.0,15885542.0,Heart1 Run1,0:51,A:199665102;C:213941735;G:204361738;T:191870055;N:324012,51,,,,199665102,213941735,204361738,191870055,324012,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,6e-05,,1e-05,,0.99989,,0.8,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37942,SRR1554476,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,510Application ReadForward1,SRP039502,,,ZF1_Heart_2.fq.gz,fastq,1013563698.0,19873798.0,Heart1 Run2,0:51,A:249913434;C:275453651;G:247166233;T:235034199;N:5996181,51,,,,249913434,275453651,247166233,235034199,5996181,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,4e-05,,2e-05,,0.99997,,0.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37991,SRR1265766,SRX529160,SRS598857,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,,Heart Replicate 3 sRNAseq,GSM1376649,,source name:Heart|tissue:Heart|genetic background:Wild type Singapore strain,Heart 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 m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Heart,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,tissue:Heart|genetic background:Wild type Singapore strain,GSM1376649,GSM1376649: Heart Replicate 3 sRNAseq; Danio rerio; miRNA Seq,GSM1376649,,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:GSM1376649,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZH008_GATCAG_L005_R1.fastq.gz,fastq,4401229692.0,57910917.0,GSM1376649 r1,0:76,A:1009381958;C:1130057881;G:1173217392;T:1088123982;N:448479,76,,,,1009381958,1130057881,1173217392,1088123982,448479,SRX529160,SRS598857,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00129,,0.00046,,0.99882,,0.51351,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Heart,Cardiovascular System
37992,SRR1265765,SRX529159,SRS598856,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,,Heart Replicate 2 sRNAseq,GSM1376648,,source name:Heart|tissue:Heart|genetic background:Wild type Singapore strain,Heart 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 m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Heart,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,tissue:Heart|genetic background:Wild type Singapore strain,GSM1376648,GSM1376648: Heart Replicate 2 sRNAseq; Danio rerio; miRNA Seq,GSM1376648,,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:GSM1376648,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZH007_ACTTGA_L005_R1.fastq.gz,fastq,3202357508.0,42136283.0,GSM1376648 r1,0:76,A:666309720;C:845347679;G:846066601;T:844306103;N:327405,76,,,,666309720,845347679,846066601,844306103,327405,SRX529159,SRS598856,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00042,,3e-05,,0.99924,,0.56521,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Heart,Cardiovascular System
37993,SRR1265764,SRX529158,SRS598855,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,,Heart Replicate 1 sRNAseq,GSM1376647,,source name:Heart|tissue:Heart|genetic background:Wild type Singapore strain,Heart 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 m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Heart,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,tissue:Heart|genetic background:Wild type Singapore strain,GSM1376647,GSM1376647: Heart Replicate 1 sRNAseq; Danio rerio; miRNA Seq,GSM1376647,,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:GSM1376647,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZH002_CAGATC_L005_R1.fastq.gz,fastq,3777814232.0,49708082.0,GSM1376647 r1,0:76,A:791204432;C:1050679958;G:1001897360;T:933655799;N:376683,76,,,,791204432,1050679958,1001897360,933655799,376683,SRX529158,SRS598855,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00034,,4e-05,,0.99943,,0.62264,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Heart,Cardiovascular System
50757,SRR8305610,SRX5120156,SRS4121979,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,AgeCtr5Month#3,,breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#3|BioSampleModel:Model organism or animal,,,,,,,,,Healthy 5months rep3 miRNA,8990,8990,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8990_S16_L008_R1_001.fastq.gz,fastq,698736950.0,13974739.0,SID8990 S16 L008 R1 001.fastq.gz,0:50,A:131989113;C:176394830;G:226656872;T:163673496;N:22639,50,,,,131989113,176394830,226656872,163673496,22639,SRX5120156,SRS4121979,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00317,,0.00059,,0.99632,,0.624,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50758,SRR8305611,SRX5120155,SRS4121983,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,AgeCtr45dpi#2,,breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr45dpi rep2 miRNA,8986,8986,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8986_S11_L007_R1_001.fastq.gz,fastq,167880450.0,3357609.0,SID8986 S11 L007 R1 001.fastq.gz,0:50,A:31714312;C:42386139;G:55132141;T:38634835;N:13023,50,,,,31714312,42386139,55132141,38634835,13023,SRX5120155,SRS4121983,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00595,,0.00101,,0.99685,,0.70197,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50759,SRR8305612,SRX5120154,SRS4121982,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,AgeCtr45dpi#3,,breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr45dpi rep3 miRNA,8987,8987,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8987_S12_L007_R1_001.fastq.gz,fastq,58209250.0,1164185.0,SID8987 S12 L007 R1 001.fastq.gz,0:50,A:11149995;C:14754333;G:18974261;T:13326125;N:4536,50,,,,11149995,14754333,18974261,13326125,4536,SRX5120154,SRS4121982,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00501,,0.00068,,0.99778,,0.66509,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50760,SRR8305613,SRX5120153,SRS4121976,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,120dpi#2,,breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,120dpi rep2 miRNA,6025,6025,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6025_S29_L005_R1_001.fastq.gz,fastq,920379950.0,18407599.0,SID6025 S29 L005 R1 001.fastq.gz,0:50,A:197341487;C:229231195;G:273629822;T:220038506;N:138940,50,,,,197341487,229231195,273629822,220038506,138940,SRX5120153,SRS4121976,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01344,,0.00253,,0.99557,,0.74965,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50761,SRR8305614,SRX5120152,SRS4121978,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,120dpi#3,,breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,120dpi rep3 miRNA,6026,6026,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6026_S26_L005_R1_001.fastq.gz,fastq,889209550.0,17784191.0,SID6026 S26 L005 R1 001.fastq.gz,0:50,A:185835825;C:227166683;G:267016163;T:209056255;N:134624,50,,,,185835825,227166683,267016163,209056255,134624,SRX5120152,SRS4121978,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02108,,0.00333,,0.9945,,0.72482,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50762,SRR8305615,SRX5120151,SRS4121975,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,60dpi#3,,breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,60dpi rep3 miRNA,6023,6023,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6023_S25_L005_R1_001.fastq.gz,fastq,807865300.0,16157306.0,SID6023 S25 L005 R1 001.fastq.gz,0:50,A:178927964;C:196404816;G:231871602;T:200541868;N:119050,50,,,,178927964,196404816,231871602,200541868,119050,SRX5120151,SRS4121975,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01977,,0.00475,,0.99381,,0.76643,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50763,SRR8305616,SRX5120150,SRS4121977,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,120dpi#1,,breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,120dpi rep1 miRNA,6024,6024,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6024_S27_L005_R1_001.fastq.gz,fastq,976958950.0,19539179.0,SID6024 S27 L005 R1 001.fastq.gz,0:50,A:207562906;C:245776777;G:289761611;T:233711355;N:146301,50,,,,207562906,245776777,289761611,233711355,146301,SRX5120150,SRS4121977,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.024,,0.00503,,0.99415,,0.68714,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50764,SRR8305617,SRX5120149,SRS4121973,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,60dpi#1,,breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,60dpi rep1 miRNA,6021,6021,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6021_S30_L005_R1_001.fastq.gz,fastq,822399250.0,16447985.0,SID6021 S30 L005 R1 001.fastq.gz,0:50,A:179285741;C:203624280;G:242490523;T:196874923;N:123783,50,,,,179285741,203624280,242490523,196874923,123783,SRX5120149,SRS4121973,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00298,,0.00065,,0.99614,,0.7096,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50765,SRR8305618,SRX5120148,SRS4121974,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,60dpi#2,,breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,60dpi rep2 miRNA,6022,6022,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6022_S28_L005_R1_001.fastq.gz,fastq,1185285550.0,23705711.0,SID6022 S28 L005 R1 001.fastq.gz,0:50,A:263566408;C:289358565;G:345225328;T:286957646;N:177603,50,,,,263566408,289358565,345225328,286957646,177603,SRX5120148,SRS4121974,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00543,,0.00143,,0.99655,,0.72969,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50766,SRR8305619,SRX5120147,SRS4121969,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,45dpi#2,,breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,45dpi rep2 miRNA,6019,6019,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6019_S24_L004_R1_001.fastq.gz,fastq,1665628850.0,33312577.0,SID6019 S24 L004 R1 001.fastq.gz,0:50,A:345040451;C:410823238;G:503499843;T:406069175;N:196143,50,,,,345040451,410823238,503499843,406069175,196143,SRX5120147,SRS4121969,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01832,,0.00329,,0.99381,,0.74442,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50767,SRR8305620,SRX5120146,SRS4121972,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,45dpi#3,,breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,45dpi rep3 miRNA,6020,6020,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6020_S19_L004_R1_001.fastq.gz,fastq,1077141150.0,21542823.0,SID6020 S19 L004 R1 001.fastq.gz,0:50,A:209184554;C:272965854;G:342027609;T:252836621;N:126512,50,,,,209184554,272965854,342027609,252836621,126512,SRX5120146,SRS4121972,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02255,,0.0041,,0.9932,,0.70804,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50768,SRR8305621,SRX5120145,SRS4121971,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,30dpi#3,,breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,30dpi rep3 miRNA,6017,6017,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6017_S22_L004_R1_001.fastq.gz,fastq,1471641150.0,29432823.0,SID6017 S22 L004 R1 001.fastq.gz,0:50,A:286808307;C:377070243;G:450396816;T:357191320;N:174464,50,,,,286808307,377070243,450396816,357191320,174464,SRX5120145,SRS4121971,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00948,,0.00145,,0.99261,,0.69419,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50769,SRR8305622,SRX5120144,SRS4121970,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,45dpi#1,,breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,45dpi rep1 miRNA,6018,6018,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6018_S23_L004_R1_001.fastq.gz,fastq,1354764100.0,27095282.0,SID6018 S23 L004 R1 001.fastq.gz,0:50,A:268591138;C:340728679;G:421161801;T:324122996;N:159486,50,,,,268591138,340728679,421161801,324122996,159486,SRX5120144,SRS4121970,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.0221,,0.00361,,0.99371,,0.69289,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50770,SRR8305623,SRX5120143,SRS4121980,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,AgeCtr5Month#1,,breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#1|BioSampleModel:Model organism or animal,,,,,,,,,Healthy 5months rep1 miRNA,8988,8988,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8988_S14_L008_R1_001.fastq.gz,fastq,55133800.0,1102676.0,SID8988 S14 L008 R1 001.fastq.gz,0:50,A:10235345;C:14001041;G:17872491;T:13023101;N:1822,50,,,,10235345,14001041,17872491,13023101,1822,SRX5120143,SRS4121980,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01094,,0.00175,,0.98953,,0.60545,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50771,SRR8305624,SRX5120142,SRS4122008,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,1dpi#3,,breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,1dpi rep3 miRNA,6002,6002,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6002_S5_L001_R1_001.fastq.gz,fastq,1578002200.0,31560044.0,SID6002 S5 L001 R1 001.fastq.gz,0:50,A:345828316;C:403094159;G:472136222;T:356835497;N:108006,50,,,,345828316,403094159,472136222,356835497,108006,SRX5120142,SRS4122008,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.07196,,0.01204,,0.98628,,0.6936,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50772,SRR8305625,SRX5120141,SRS4122009,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,1dpi#2,,breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,1dpi rep2 miRNA,6001,6001,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6001_S4_L001_R1_001.fastq.gz,fastq,1234803500.0,24696070.0,SID6001 S4 L001 R1 001.fastq.gz,0:50,A:251952768;C:310000103;G:374403246;T:298358838;N:88545,50,,,,251952768,310000103,374403246,298358838,88545,SRX5120141,SRS4122009,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.05028,,0.0095,,0.98837,,0.67564,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50773,SRR8305626,SRX5120140,SRS4122010,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,4dpi#2,,breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,4dpi rep2 miRNA,6004,6004,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6004_S8_L002_R1_001.fastq.gz,fastq,1250169750.0,25003395.0,SID6004 S8 L002 R1 001.fastq.gz,0:50,A:240593316;C:315540319;G:393819940;T:300120501;N:95674,50,,,,240593316,315540319,393819940,300120501,95674,SRX5120140,SRS4122010,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02656,,0.00415,,0.99155,,0.62344,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50774,SRR8305627,SRX5120139,SRS4122011,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,4dpi#1,,breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,4dpi rep1 miRNA,6003,6003,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6003_S7_L002_R1_001.fastq.gz,fastq,1563660750.0,31273215.0,SID6003 S7 L002 R1 001.fastq.gz,0:50,A:314953051;C:395817158;G:476754857;T:376018422;N:117262,50,,,,314953051,395817158,476754857,376018422,117262,SRX5120139,SRS4122011,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.04092,,0.00568,,0.9895,,0.69059,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50775,SRR8305628,SRX5120138,SRS4122004,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,sham#2,,breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#2|BioSampleModel:Model organism or animal,,,,,,,,,sham rep2 miRNA,5998,5998,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID5998_S6_L001_R1_001.fastq.gz,fastq,1588288100.0,31765762.0,SID5998 S6 L001 R1 001.fastq.gz,0:50,A:342796715;C:390105841;G:464467318;T:390803929;N:114297,50,,,,342796715,390105841,464467318,390803929,114297,SRX5120138,SRS4122004,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.03765,,0.00775,,0.99371,,0.71003,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50776,SRR8305629,SRX5120137,SRS4122005,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,sham#1,,breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#1|BioSampleModel:Model organism or animal,,,,,,,,,sham rep1 miRNA,5997,5997,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID5997_S1_L005_R1_001.fastq.gz,fastq,1551989700.0,31039794.0,SID5997 S1 L005 R1 001.fastq.gz,0:50,A:322274392;C:384135688;G:460825098;T:384698486;N:56036,50,,,,322274392,384135688,460825098,384698486,56036,SRX5120137,SRS4122005,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.0173,,0.00355,,0.99571,,0.71717,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50777,SRR8305630,SRX5120136,SRS4122006,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,1dpi#1,,breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,1dpi rep1 miRNA,6000,6000,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6000_S3_L001_R1_001.fastq.gz,fastq,1782388700.0,35647774.0,SID6000 S3 L001 R1 001.fastq.gz,0:50,A:346286113;C:454398380;G:577494456;T:404083801;N:125950,50,,,,346286113,454398380,577494456,404083801,125950,SRX5120136,SRS4122006,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02786,,0.00537,,0.99103,,0.80383,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50778,SRR8305631,SRX5120135,SRS4122007,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,sham#3,,breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#3|BioSampleModel:Model organism or animal,,,,,,,,,sham rep3 miRNA,5999,5999,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID5999_S2_L001_R1_001.fastq.gz,fastq,1062556900.0,21251138.0,SID5999 S2 L001 R1 001.fastq.gz,0:50,A:217053290;C:267053521;G:321242631;T:257131790;N:75668,50,,,,217053290,267053521,321242631,257131790,75668,SRX5120135,SRS4122007,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01276,,0.00266,,0.99206,,0.76992,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50779,SRR8305632,SRX5120134,SRS4121981,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,AgeCtr5Month#2,,breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#2|BioSampleModel:Model organism or animal,,,,,,,,,Healthy 5months rep2 miRNA,8989,8989,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8989_S15_L008_R1_001.fastq.gz,fastq,1238593550.0,24771871.0,SID8989 S15 L008 R1 001.fastq.gz,0:50,A:234342146;C:315041073;G:406169561;T:283000578;N:40192,50,,,,234342146,315041073,406169561,283000578,40192,SRX5120134,SRS4121981,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.0018,,0.00029,,0.99707,,0.75503,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50780,SRR8305633,SRX5120133,SRS4122012,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,7dpi#1,,breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,7dpi rep1 miRNA,6006,6006,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6006_S10_L002_R1_001.fastq.gz,fastq,2236210750.0,44724215.0,SID6006 S10 L002 R1 001.fastq.gz,0:50,A:418358075;C:559212196;G:698422326;T:560042907;N:175246,50,,,,418358075,559212196,698422326,560042907,175246,SRX5120133,SRS4122012,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.03621,,0.00542,,0.99026,,0.6579,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2018-12-13,Adult,Adult,Heart,Cardiovascular System
50781,SRR8305634,SRX5120132,SRS4122013,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,4dpi#3,,breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,4dpi rep3 miRNA,6005,6005,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6005_S9_L002_R1_001.fastq.gz,fastq,1055547700.0,21110954.0,SID6005 S9 L002 R1 001.fastq.gz,0:50,A:206864874;C:267418316;G:328346657;T:252837721;N:80132,50,,,,206864874,267418316,328346657,252837721,80132,SRX5120132,SRS4122013,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.03345,,0.00484,,0.99178,,0.62838,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50782,SRR8305635,SRX5120131,SRS4122001,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,AgeCtr45dpi#1,,breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr45dpi rep1 miRNA,8985,8985,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8985_S10_L007_R1_001.fastq.gz,fastq,157438950.0,3148779.0,SID8985 S10 L007 R1 001.fastq.gz,0:50,A:29907011;C:39967744;G:51803529;T:35747899;N:12767,50,,,,29907011,39967744,51803529,35747899,12767,SRX5120131,SRS4122001,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00551,,0.00091,,0.99758,,0.68992,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50783,SRR8305636,SRX5120130,SRS4122003,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,AgeCtr120dpi#3,,breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr120dpi rep3 miRNA,8984,8984,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8984_S8_L006_R1_001.fastq.gz,fastq,527926150.0,10558523.0,SID8984 S8 L006 R1 001.fastq.gz,0:50,A:100249504;C:134536518;G:170369710;T:122751228;N:19190,50,,,,100249504,134536518,170369710,122751228,19190,SRX5120130,SRS4122003,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00248,,0.00046,,0.99748,,0.67021,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50784,SRR8305637,SRX5120129,SRS4121987,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,AgeCtr160dpi#3,,breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr160dpi rep3 miRNA,8981,8981,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8981_S4_L005_R1_001.fastq.gz,fastq,461202550.0,9224051.0,SID8981 S4 L005 R1 001.fastq.gz,0:50,A:93413883;C:114608387;G:142367379;T:110796282;N:16619,50,,,,93413883,114608387,142367379,110796282,16619,SRX5120129,SRS4121987,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01441,,0.00274,,0.99579,,0.75424,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50785,SRR8305638,SRX5120128,SRS4121989,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,AgeCtr160dpi#2,,breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr160dpi rep2 miRNA,8980,8980,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8980_S3_L005_R1_001.fastq.gz,fastq,709335250.0,14186705.0,SID8980 S3 L005 R1 001.fastq.gz,0:50,A:139628736;C:176770611;G:222154342;T:170755378;N:26183,50,,,,139628736,176770611,222154342,170755378,26183,SRX5120128,SRS4121989,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01323,,0.00258,,0.99628,,0.8087,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50786,SRR8305639,SRX5120127,SRS4121984,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,AgeCtr120dpi#2,,breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr120dpi rep2 miRNA,8983,8983,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8983_S7_L006_R1_001.fastq.gz,fastq,110092850.0,2201857.0,SID8983 S7 L006 R1 001.fastq.gz,0:50,A:20832150;C:27890992;G:35337269;T:26028356;N:4083,50,,,,20832150,27890992,35337269,26028356,4083,SRX5120127,SRS4121984,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00659,,0.00124,,0.99464,,0.64092,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50787,SRR8305640,SRX5120126,SRS4121985,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,AgeCtr120dpi#1,,breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr120dpi rep1 miRNA,8982,8982,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8982_S6_L006_R1_001.fastq.gz,fastq,274783000.0,5495660.0,SID8982 S6 L006 R1 001.fastq.gz,0:50,A:51202860;C:70356196;G:89068979;T:64144960;N:10005,50,,,,51202860,70356196,89068979,64144960,10005,SRX5120126,SRS4121985,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00736,,0.00142,,0.99519,,0.67978,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50788,SRR8305641,SRX5120125,SRS4121991,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,160dpi#2,,breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,160dpi rep2 miRNA,7273,7273,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID7273_S13_L008_R1_001.fastq.gz,fastq,1562494050.0,31249881.0,SID7273 S13 L008 R1 001.fastq.gz,0:50,A:322066209;C:401076329;G:458040591;T:381260838;N:50083,50,,,,322066209,401076329,458040591,381260838,50083,SRX5120125,SRS4121991,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.00546,,0.00063,,0.99758,,0.63443,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50789,SRR8305642,SRX5120124,SRS4121992,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,160dpi#1,,breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,160dpi rep1 miRNA,6754,6754,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6754_S12_L002_R1_001.fastq.gz,fastq,970614525.0,12941527.0,SID6754 S12 L002 R1 001.fastq.gz,0:75,A:226197330;C:263276797;G:244870748;T:236180457;N:89193,75,,,,226197330,263276797,244870748,236180457,89193,SRX5120124,SRS4121992,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,6e-05,,1e-05,,0.99985,,0.75,,75,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50790,SRR8305643,SRX5120123,SRS4121993,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,AgeCtr160dpi#1,,breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,AgeMatchCtr160dpi rep1 miRNA,8979,8979,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID8979_S2_L005_R1_001.fastq.gz,fastq,1191571700.0,23831434.0,SID8979 S2 L005 R1 001.fastq.gz,0:50,A:231936155;C:298463393;G:377425675;T:283702936;N:43541,50,,,,231936155,298463393,377425675,283702936,43541,SRX5120123,SRS4121993,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.01636,,0.00334,,0.99478,,0.78529,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50791,SRR8305644,SRX5120122,SRS4121990,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,160dpi#3,,breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,160dpi rep3 miRNA,7274,7274,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID7274_S18_L003_R1_001.fastq.gz,fastq,587672100.0,7835628.0,SID7274 S18 L003 R1 001.fastq.gz,0:75,A:128228313;C:152211828;G:156460760;T:150725049;N:46150,75,,,,128228313,152211828,156460760,150725049,46150,SRX5120122,SRS4121990,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,9e-05,,1e-05,,0.99975,,0.46153,,75,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50792,SRR8305645,SRX5120121,SRS4122000,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,21dpi#3,,breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,21dpi rep3 miRNA,6014,6014,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6014_S18_L003_R1_001.fastq.gz,fastq,470984100.0,9419682.0,SID6014 S18 L003 R1 001.fastq.gz,0:50,A:90590892;C:122988758;G:143456400;T:113917917;N:30133,50,,,,90590892,122988758,143456400,113917917,30133,SRX5120121,SRS4122000,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02203,,0.00201,,0.99312,,0.39653,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2018-12-13,Adult,Adult,Heart,Cardiovascular System
50793,SRR8305646,SRX5120120,SRS4122002,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,21dpi#2,,breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,21dpi rep2 miRNA,6013,6013,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6013_S17_L003_R1_001.fastq.gz,fastq,785630400.0,15712608.0,SID6013 S17 L003 R1 001.fastq.gz,0:50,A:152017861;C:201679585;G:240972325;T:190910430;N:50199,50,,,,152017861,201679585,240972325,190910430,50199,SRX5120120,SRS4122002,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02519,,0.00378,,0.99373,,0.40787,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50794,SRR8305647,SRX5120119,SRS4121999,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,21dpi#1,,breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,21dpi rep1 miRNA,6012,6012,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6012_S16_L003_R1_001.fastq.gz,fastq,494552600.0,9891052.0,SID6012 S16 L003 R1 001.fastq.gz,0:50,A:95336093;C:129024365;G:149497515;T:120663807;N:30820,50,,,,95336093,129024365,149497515,120663807,30820,SRX5120119,SRS4121999,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.04208,,0.00538,,0.992,,0.61501,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50795,SRR8305648,SRX5120118,SRS4121998,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,14dpi#3,,breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,14dpi rep3 miRNA,6011,6011,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6011_S15_L003_R1_001.fastq.gz,fastq,578164050.0,11563281.0,SID6011 S15 L003 R1 001.fastq.gz,0:50,A:109934197;C:149003532;G:179264553;T:139924815;N:36953,50,,,,109934197,149003532,179264553,139924815,36953,SRX5120118,SRS4121998,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.0225,,0.00372,,0.9906,,0.61747,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Undetermined,Undetermined,Heart,Cardiovascular System
50796,SRR8305649,SRX5120117,SRS4121996,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,14dpi#2,,breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,14dpi rep2 miRNA,6010,6010,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6010_S14_L003_R1_001.fastq.gz,fastq,682820200.0,13656404.0,SID6010 S14 L003 R1 001.fastq.gz,0:50,A:132413613;C:177691857;G:213067602;T:159602931;N:44197,50,,,,132413613,177691857,213067602,159602931,44197,SRX5120117,SRS4121996,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02361,,0.00321,,0.99281,,0.46548,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Undetermined,Undetermined,Heart,Cardiovascular System
50797,SRR8305650,SRX5120116,SRS4121997,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,14dpi#1,,breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,14dpi rep1 miRNA,6009,6009,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6009_S5_L006_R1_001.fastq.gz,fastq,645018650.0,12900373.0,SID6009 S5 L006 R1 001.fastq.gz,0:50,A:121217579;C:170403284;G:199790376;T:153583951;N:23460,50,,,,121217579,170403284,199790376,153583951,23460,SRX5120116,SRS4121997,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.02637,,0.00359,,0.99095,,0.50364,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Undetermined,Undetermined,Heart,Cardiovascular System
50798,SRR8305651,SRX5120115,SRS4121994,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 3,,7dpi#3,,breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#3|BioSampleModel:Model organism or animal,,,,,,,,,7dpi rep3 miRNA,6008,6008,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6008_S11_L002_R1_001.fastq.gz,fastq,1016249900.0,20324998.0,SID6008 S11 L002 R1 001.fastq.gz,0:50,A:196023277;C:256234305;G:315577111;T:248336546;N:78661,50,,,,196023277,256234305,315577111,248336546,78661,SRX5120115,SRS4121994,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.03415,,0.00416,,0.98981,,0.66977,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50799,SRR8305652,SRX5120114,SRS4121995,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,7dpi#2,,breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,7dpi rep2 miRNA,6007,6007,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6007_S12_L002_R1_001.fastq.gz,fastq,1405772250.0,28115445.0,SID6007 S12 L002 R1 001.fastq.gz,0:50,A:270753665;C:356955121;G:444759435;T:333191995;N:112034,50,,,,270753665,356955121,444759435,333191995,112034,SRX5120114,SRS4121995,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.0195,,0.00225,,0.99291,,0.65233,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2018-12-13,Adult,Adult,Heart,Cardiovascular System
50800,SRR8305653,SRX5120113,SRS4121986,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 2,,30dpi#2,,breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#2|BioSampleModel:Model organism or animal,,,,,,,,,30dpi rep2 miRNA,6016,6016,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6016_S21_L004_R1_001.fastq.gz,fastq,1317403300.0,26348066.0,SID6016 S21 L004 R1 001.fastq.gz,0:50,A:248382887;C:331301718;G:402502543;T:335061139;N:155013,50,,,,248382887,331301718,402502543,335061139,155013,SRX5120113,SRS4121986,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.05594,,0.00908,,0.98569,,0.68185,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System
50801,SRR8305654,SRX5120112,SRS4121988,SRP173044,PRJNA509429,Delineating the transcriptomic response during Zebrafish heart regeneration,PRJNA509429,Other,Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.,,pubmed:30597924,Replicate 1,,30dpi#1,,breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#1|BioSampleModel:Model organism or animal,,,,,,,,,30dpi rep1 miRNA,6015,6015,miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP173044,,,SID6015_S20_L004_R1_001.fastq.gz,fastq,1342409800.0,26848196.0,SID6015 S20 L004 R1 001.fastq.gz,0:50,A:256149333;C:337592303;G:419179623;T:329329916;N:158625,50,,,,256149333,337592303,419179623,329329916,158625,SRX5120112,SRS4121988,SRA822004,University of Freiburg|Institute of Molecular Medicine and Cell Research,University of Freiburg DeCaRe,1,0.03123,,0.00479,,0.98999,,0.62344,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,Germany,2019-04-30,Adult,Adult,Heart,Cardiovascular System