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
37134,SRR997335,SRX355601,SRS483796,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep4,GSM1234963,,source name:Heart  Control|tissue:heart,Heart  Control  rep4,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234963,GSM1234963: Heart  Control  rep4; Danio rerio; RNA Seq,GSM1234963,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234963,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_7_sequence.txt.gz,fastq,1111882122.0,28509798.0,GSM1234963 r1,0:39,A:239964076;C:229590501;G:337557042;T:303257677;N:1512826,39,,,,239964076,229590501,337557042,303257677,1512826,SRX355601,SRS483796,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.11195,,0.03776,,0.98871,,0.16576,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37135,SRR997334,SRX355600,SRS483795,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep3,GSM1234962,,source name:Heart  Control|tissue:heart,Heart  Control  rep3,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234962,GSM1234962: Heart  Control  rep3; Danio rerio; RNA Seq,GSM1234962,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234962,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_6_sequence.txt.gz,fastq,1221305046.0,31315514.0,GSM1234962 r1,0:39,A:263520584;C:251263128;G:372262308;T:332218529;N:2040497,39,,,,263520584,251263128,372262308,332218529,2040497,SRX355600,SRS483795,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.11552,,0.03865,,0.98679,,0.1927,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37136,SRR997333,SRX355599,SRS483794,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep2,GSM1234961,,source name:Heart  Control|tissue:heart,Heart  Control  rep2,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234961,GSM1234961: Heart  Control  rep2; Danio rerio; RNA Seq,GSM1234961,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234961,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,R2D2_0122_s_7_sequence.txt.gz,fastq,1462542939.0,37501101.0,GSM1234961 r1,0:39,A:313173840;C:298865755;G:440814004;T:409066990;N:622350,39,,,,313173840,298865755,440814004,409066990,622350,SRX355599,SRS483794,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.01745,,0.00554,,0.99101,,0.42928,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37137,SRR997332,SRX355598,SRS483793,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep1,GSM1234960,,source name:Heart  Control|tissue:heart,Heart  Control  rep1,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234960,GSM1234960: Heart  Control  rep1; Danio rerio; RNA Seq,GSM1234960,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234960,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,R2D2_0122_s_6_sequence.txt.gz,fastq,1447346355.0,37111445.0,GSM1234960 r1,0:39,A:311132663;C:297266985;G:441400778;T:396960907;N:585022,39,,,,311132663,297266985,441400778,396960907,585022,SRX355598,SRS483793,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.06118,,0.01997,,0.98752,,0.43741,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37138,SRR997331,SRX355597,SRS483792,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep4,GSM1234959,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep4,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234959,GSM1234959: Heart  Resected  rep4; Danio rerio; RNA Seq,GSM1234959,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234959,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_5_sequence.txt.gz,fastq,703519557.0,18038963.0,GSM1234959 r1,0:39,A:142685665;C:144259439;G:215526965;T:199924689;N:1122799,39,,,,142685665,144259439,215526965,199924689,1122799,SRX355597,SRS483792,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.00172,,0.00045,,0.99738,,0.34873,,39,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37139,SRR997330,SRX355596,SRS483791,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep3,GSM1234958,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep3,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234958,GSM1234958: Heart  Resected  rep3; Danio rerio; RNA Seq,GSM1234958,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234958,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_4_sequence.txt.gz,fastq,918978177.0,23563543.0,GSM1234958 r1,0:39,A:188056254;C:191217660;G:283318445;T:255042736;N:1343082,39,,,,188056254,191217660,283318445,255042736,1343082,SRX355596,SRS483791,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.09453,,0.03085,,0.98559,,0.18337,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37140,SRR997329,SRX355595,SRS483789,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep2,GSM1234957,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep2,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234957,GSM1234957: Heart  Resected  rep2; Danio rerio; RNA Seq,GSM1234957,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234957,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,R2D2_0122_s_5_sequence.txt.gz,fastq,1420874247.0,36432673.0,GSM1234957 r1,0:39,A:290914118;C:295973738;G:440368910;T:393019696;N:597785,39,,,,290914118,295973738,440368910,393019696,597785,SRX355595,SRS483789,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.00472,,0.00131,,0.99431,,0.42832,,39,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37141,SRR997328,SRX355594,SRS483790,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep1,GSM1234956,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep1,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234956,GSM1234956: Heart  Resected  rep1; Danio rerio; RNA Seq,GSM1234956,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234956,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0054_s_8_sequence.txt.gz,fastq,1073339514.0,27521526.0,GSM1234956 r1,0:39,A:223670054;C:219603945;G:328718329;T:300891777;N:455409,39,,,,223670054,219603945,328718329,300891777,455409,SRX355594,SRS483790,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.05133,,0.01643,,0.9893,,0.25792,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37991,SRR1265766,SRX529160,SRS598857,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Heart Replicate 3 sRNAseq,GSM1376649,,source name:Heart|tissue:Heart|genetic background:Wild type   Singapore strain,Heart Replicate 3 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <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,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,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,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 predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult 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,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,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,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,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,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,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,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,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,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,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,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,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