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67 rows where experiment.library_strategy = "miRNA-Seq" and tissue_curation_coarse = "Cardiovascular System"

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devstage_curation 5

devstage_curation_coarse 4

experiment.library_selection 3

tissue_curation 2

technology 2

experiment.platform 2

tissue_curation_coarse 1

  • Cardiovascular System · 67 ✖

experiment.library_strategy 1

  • miRNA-Seq · 67 ✖

experiment.library_source 1

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
37923 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. 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 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. 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 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. 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
39611 39611 SRR1873569 SRX915249 SRS870225 SRP056014 PRJNA277780 Identification of small non coding RNAs in zebrafish GSE66718 Transcriptome Analysis MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.   pubmed:26694924   heart GSM1630513   source name:adult heart 1 year old|strain/background:AB|genotype/variation:wild type|tissue:heart|developmental stage:adult|age:1 year heart Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs… adult heart 1 year old   100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle. strain/background:AB|genotype/variation:wild type|tissue:heart|developmental stage:adult|age:1 year GSM1630513 GSM1630513: heart; Danio rerio; miRNA Seq GSM1630513   1 100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. GEO Accession:GSM1630513 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE LS454 454 GS FLX   SRP056014         39500.0 711.0 GSM1630513 r1 0:4 1:51.56 A:11300;C:9125;G:9195;T:9835;N:45 4 51     11300 9125 9195 9835 45 SRX915249 SRS870225 SRA246117 GEO University of Aveiro 1 0.0   0.0   1.0       53   T   under 1.2% mapping rate legacy early 3prime size_fractionation unknown bulk other_seq 454   Portugal 2015-03-09 Adult Adult Heart Cardiovascular System
40972 40972 SRR3498294 SRX1756840 SRS1433371 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 72hpf E2 GSM2150819   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP NoEndo 72hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150819 GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq GSM2150819   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150819 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_72hpf_E2.fastq.gz fastq 797509876.0 10493551.0 GSM2150819 r1 0:76 A:182564842;C:199547592;G:199064466;T:216287390;N:45586 76       182564842 199547592 199064466 216287390 45586 SRX1756840 SRS1433371 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40973 40973 SRR3498293 SRX1756839 SRS1433370 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 72hpf E1 GSM2150818   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP NoEndo 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150818 GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq GSM2150818   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150818 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_72hpf_E1.fastq.gz fastq 1864172232.0 24528582.0 GSM2150818 r1 0:76 A:426671762;C:469538477;G:458132395;T:509711525;N:118073 76       426671762 469538477 458132395 509711525 118073 SRX1756839 SRS1433370 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40974 40974 SRR3498292 SRX1756838 SRS1433369 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 6dpf E1 GSM2150817   source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP NoEndo 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6dpf|tissue:Endothelial|stain:GFP GSM2150817 GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq GSM2150817   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150817 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_6dpf_E1.fastq.gz fastq 1414849364.0 18616439.0 GSM2150817 r1 0:76 A:315250036;C:366906308;G:364673112;T:367938758;N:81150 76       315250036 366906308 364673112 367938758 81150 SRX1756838 SRS1433369 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40975 40975 SRR3498291 SRX1756837 SRS1433368 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 48hpf E2 GSM2150816   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP NoEndo 48hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150816 GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq GSM2150816   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150816 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_48hpf_E2.fastq.gz fastq 553364740.0 7281115.0 GSM2150816 r1 0:76 A:129173344;C:134804122;G:141026546;T:148331467;N:29261 76       129173344 134804122 141026546 148331467 29261 SRX1756837 SRS1433368 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   0.99997   0.0   76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40976 40976 SRR3498290 SRX1756836 SRS1433367 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 48hpf E1 GSM2150815   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP NoEndo 48hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150815 GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq GSM2150815   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150815 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_48hpf_E1.fastq.gz fastq 1204752152.0 15852002.0 GSM2150815 r1 0:76 A:297517299;C:293969730;G:317491224;T:295696492;N:77407 76       297517299 293969730 317491224 295696492 77407 SRX1756836 SRS1433367 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40977 40977 SRR3498289 SRX1756835 SRS1433366 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 24hpf E1 GSM2150814   source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP NoEndo 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24hpf|tissue:Endothelial|stain:GFP GSM2150814 GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq GSM2150814   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150814 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_24hpf_E1.fastq.gz fastq 1422085704.0 18711654.0 GSM2150814 r1 0:76 A:347700492;C:356065333;G:376424133;T:341806001;N:89745 76       347700492 356065333 376424133 341806001 89745 SRX1756835 SRS1433366 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
40978 40978 SRR3498288 SRX1756834 SRS1433365 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 72hpf E2 GSM2150813   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP Endo 72hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150813 GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq GSM2150813   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150813 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_72hpf_E2.fastq.gz fastq 438128980.0 5764855.0 GSM2150813 r1 0:76 A:101851745;C:114159902;G:115733669;T:106360221;N:23443 76       101851745 114159902 115733669 106360221 23443 SRX1756834 SRS1433365 SRA424808 GEO Internal Medicine, Yale University 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40979 40979 SRR3498287 SRX1756833 SRS1433364 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 72hpf E1 GSM2150812   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP Endo 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150812 GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq GSM2150812   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150812 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_72hpf_E1.fastq.gz fastq 1267915068.0 16683093.0 GSM2150812 r1 0:76 A:321606522;C:310505837;G:323829249;T:311892892;N:80568 76       321606522 310505837 323829249 311892892 80568 SRX1756833 SRS1433364 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40980 40980 SRR3498286 SRX1756832 SRS1433363 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 6dpf E1 GSM2150811   source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP Endo 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6dpf|tissue:Endothelial|stain:GFP GSM2150811 GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq GSM2150811   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150811 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_6dpf_E1.fastq.gz fastq 890474824.0 11716774.0 GSM2150811 r1 0:76 A:230419087;C:212029155;G:232306960;T:215672618;N:47004 76       230419087 212029155 232306960 215672618 47004 SRX1756832 SRS1433363 SRA424808 GEO Internal Medicine, Yale University 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40981 40981 SRR3498285 SRX1756831 SRS1433362 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 48hpf E2 GSM2150810   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP Endo 48hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150810 GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq GSM2150810   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150810 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_48hpf_E2.fastq.gz fastq 1254556624.0 16507324.0 GSM2150810 r1 0:76 A:316229540;C:323340793;G:307552357;T:307354555;N:79379 76       316229540 323340793 307552357 307354555 79379 SRX1756831 SRS1433362 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40982 40982 SRR3498284 SRX1756830 SRS1433361 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 48hpf E1 GSM2150809   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP Endo 48hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150809 GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq GSM2150809   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150809 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_48hpf_E1.fastq.gz fastq 1449497080.0 19072330.0 GSM2150809 r1 0:76 A:362564557;C:370330864;G:364749441;T:351760774;N:91444 76       362564557 370330864 364749441 351760774 91444 SRX1756830 SRS1433361 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40983 40983 SRR3498283 SRX1756829 SRS1433360 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 24hpf E1 GSM2150808   source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP Endo 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24hpf|tissue:Endothelial|stain:GFP GSM2150808 GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq GSM2150808   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150808 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_24hpf_E1.fastq.gz fastq 1527500440.0 20098690.0 GSM2150808 r1 0:76 A:356712587;C:354608109;G:432977038;T:383106520;N:96186 76       356712587 354608109 432977038 383106520 96186 SRX1756829 SRS1433360 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
50757 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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