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
42495,SRR5666979,SRX2902577,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells hlx1  MO rep2,3,kdrl GFP cells hlx1  MO rep2,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_hlx_8ng_48hrs_2_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_2_R2.fastq.gz,fastq fastq,1887289200.0,12581928.0,flk gfp hlx 8ng 48hrs 2 R1.fastq.gz,0:75 1:75,A:493825524;C:448630716;G:436118597;T:508410442;N:303921,75,75,,,493825524,448630716,436118597,508410442,303921,SRX2902577,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.9202,0.9216,0.09499,0.09558,0.73805,0.73878,0.48809,0.48787,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42496,SRR5666980,SRX2902576,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells hlx1  MO rep1,2,kdrl GFP cells hlx1  MO rep1,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_hlx_8ng_48hrs_1_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_1_R2.fastq.gz,fastq fastq,1561083900.0,10407226.0,flk gfp hlx 8ng 48hrs 1 R2.fastq.gz,0:75 1:75,A:412744284;C:366776465;G:356834742;T:424473871;N:254538,75,75,,,412744284,366776465,356834742,424473871,254538,SRX2902576,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.9172,0.91824,0.09957,0.09961,0.73965,0.73975,0.48906,0.48977,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42497,SRR5666981,SRX2902575,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells control 2,1,kdrl GFP cells control 2,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_48hrs_con2_R1.fastq.gz flk_gfp_48hrs_con2_R2.fastq.gz,fastq fastq,2042164500.0,13614430.0,flk gfp 48hrs con2 R1.fastq.gz,0:75 1:75,A:537008617;C:483956616;G:465380092;T:555490621;N:328554,75,75,,,537008617,483956616,465380092,555490621,328554,SRX2902575,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.91492,0.91762,0.10575,0.10669,0.75519,0.75546,0.49482,0.49617,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42498,SRR5666982,SRX2902574,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells control 1,0,kdrl GFP cells control 1,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_48hrs_con1_R2.fastq.gz flk_gfp_48hrs_con1_R1.fastq.gz,fastq fastq,1678987200.0,11193248.0,flk gfp 48hrs con1 R2.fastq.gz,0:75 1:75,A:437283407;C:401234553;G:387947515;T:452257282;N:264443,75,75,,,437283407,401234553,387947515,452257282,264443,SRX2902574,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.91593,0.91737,0.08937,0.08988,0.75607,0.75696,0.50103,0.45539,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42499,SRR5666985,SRX2902571,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,fli GFP cells hHLXOE rep 2,5,fli GFP cells hHLXOE rep 2,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,fli_gal4_uas_hlx_endo_48h_s2_R2.fastq.gz fli_gal4_uas_hlx_endo_48h_s2_R1.fastq.gz,fastq fastq,4490898450.0,29939323.0,fli gal4 uas hlx endo 48h s2 R2.fastq.gz,0:75 1:75,A:870349076;C:1346136891;G:1401796534;T:869066463;N:3549486,75,75,,,870349076,1346136891,1401796534,869066463,3549486,SRX2902571,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.5714,0.57344,0.27957,0.28321,0.85102,0.85342,0.53304,0.53368,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42500,SRR5666986,SRX2902570,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,fli GFP cells hHLXOE rep 1,4,fli GFP cells hHLXOE rep 1,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,fli_gal4_uas_hlx_endo_48h_s1_R1.fastq.gz fli_gal4_uas_hlx_endo_48h_s1_R2.fastq.gz,fastq fastq,3459602100.0,23064014.0,fli gal4 uas hlx endo 48h s1 R1.fastq.gz,0:75 1:75,A:658343595;C:1050309687;G:1097759573;T:650443491;N:2745754,75,75,,,658343595,1050309687,1097759573,650443491,2745754,SRX2902570,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.57077,0.57481,0.2173,0.2185,0.79553,0.79762,0.50405,0.48708,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
55379,SRR10323881,SRX7034716,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,10,10,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,3356658750.0,22377725.0,RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:875300673;C:782517555;G:796855605;T:901672776;N:312141,75,75,,,875300673,782517555,796855605,901672776,312141,SRX7034716,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.68437,0.73326,0.04743,0.05194,0.80241,0.80517,0.51875,0.52196,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55380,SRR10323882,SRX7034715,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,9,9,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz,fastq fastq,3459242400.0,23061616.0,RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:924400584;C:762078140;G:779330250;T:993109509;N:323917,75,75,,,924400584,762078140,779330250,993109509,323917,SRX7034715,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.67032,0.73764,0.07629,0.08303,0.80856,0.80748,0.52094,0.52695,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55381,SRR10323883,SRX7034714,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,8,8,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,3238312500.0,21588750.0,RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:881635390;C:656958401;G:673596788;T:1025824968;N:296953,75,75,,,881635390,656958401,673596788,1025824968,296953,SRX7034714,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.59623,0.72377,0.07781,0.08944,0.80608,0.8016,0.53277,0.53095,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55382,SRR10323884,SRX7034713,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,7,7,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,3255021150.0,21700141.0,RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:858912760;C:733048670;G:750496371;T:912263495;N:299854,75,75,,,858912760,733048670,750496371,912263495,299854,SRX7034713,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.65481,0.71883,0.05477,0.05995,0.7903,0.7921,0.51367,0.51188,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55383,SRR10323885,SRX7034712,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,6,6,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz,fastq fastq,2413394850.0,16089299.0,RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:660807483;C:490677840;G:505039519;T:756646234;N:223774,75,75,,,660807483,490677840,505039519,756646234,223774,SRX7034712,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.60009,0.72319,0.09185,0.10528,0.82175,0.81815,0.5234,0.51725,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55384,SRR10323886,SRX7034711,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,5,5,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,3124357200.0,20829048.0,RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:844721216;C:673572690;G:689308705;T:916479849;N:274740,75,75,,,844721216,673572690,689308705,916479849,274740,SRX7034711,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.66396,0.73861,0.09392,0.10351,0.80856,0.80797,0.53225,0.5369,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55385,SRR10323891,SRX7034706,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,4,4,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz,fastq fastq,2812593000.0,18750620.0,RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:759189725;C:611361876;G:625876145;T:815905469;N:259785,75,75,,,759189725,611361876,625876145,815905469,259785,SRX7034706,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.63609,0.70403,0.08285,0.0932,0.79847,0.79959,0.52487,0.52941,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55386,SRR10323898,SRX7034699,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  decitabine treatment in hemogenic endothelial cell 26hpf replicate 2,24,24,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz,fastq fastq,5849571450.0,38997143.0,RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:1574421853;C:1316832574;G:1315527058;T:1642305644;N:484321,75,75,,,1574421853,1316832574,1315527058,1642305644,484321,SRX7034699,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.78221,0.84034,0.0684,0.07089,0.76607,0.77025,0.50712,0.50772,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55387,SRR10323899,SRX7034698,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1,23,23,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,5656815000.0,37712100.0,RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:1487198866;C:1332723090;G:1275197163;T:1514410765;N:47285116,75,75,,,1487198866,1332723090,1275197163,1514410765,47285116,SRX7034698,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.86399,0.76012,0.0587,0.05779,0.76461,0.9105,0.49754,0.51037,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55388,SRR10323900,SRX7034697,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  VPA treatment in hemogenic endothelial cell 26hpf replicate 2,22,22,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz,fastq fastq,5978780250.0,39858535.0,RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:1580804547;C:1404640964;G:1399714637;T:1593586843;N:33259,75,75,,,1580804547,1404640964,1399714637,1593586843,33259,SRX7034697,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.92216,0.92477,0.04155,0.04126,0.74537,0.7512,0.48148,0.49049,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55389,SRR10323901,SRX7034696,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1,21,21,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,8777730900.0,58518206.0,RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:2331650285;C:2053244561;G:2042022053;T:2350762388;N:51613,75,75,,,2331650285,2053244561,2042022053,2350762388,51613,SRX7034696,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.92143,0.92455,0.04604,0.04567,0.73361,0.73923,0.4802,0.48613,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55390,SRR10323902,SRX7034695,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,3,3,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,3613041150.0,24086941.0,RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:972417798;C:795483066;G:808300399;T:1036510724;N:329163,75,75,,,972417798,795483066,808300399,1036510724,329163,SRX7034695,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.66853,0.7231,0.08329,0.0907,0.78953,0.79131,0.51481,0.52637,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55391,SRR10323903,SRX7034694,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2,20,20,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,7211828100.0,48078854.0,RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:1904350731;C:1693709371;G:1687946675;T:1925778331;N:42992,75,75,,,1904350731,1693709371,1687946675,1925778331,42992,SRX7034694,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.91819,0.92224,0.03958,0.03841,0.75584,0.76161,0.46923,0.46415,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55392,SRR10323904,SRX7034693,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for VPA treatment in hemogenic endothelial cell 26hpf replicate 1,19,19,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,8021297850.0,53475319.0,RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:2121666298;C:1880005094;G:1872358379;T:2147221627;N:46452,75,75,,,2121666298,1880005094,1872358379,2147221627,46452,SRX7034693,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.91273,0.91897,0.0437,0.04345,0.75485,0.76037,0.46259,0.47199,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55393,SRR10323905,SRX7034692,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,18,18,TruSeq stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,4925792850.0,32838619.0,RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:1327496924;C:1143172265;G:1121827107;T:1332765205;N:531349,75,75,,,1327496924,1143172265,1121827107,1332765205,531349,SRX7034692,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.9235,0.923,0.07189,0.07157,0.74576,0.7486,0.46424,0.46997,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55394,SRR10323906,SRX7034691,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,17,17,TruSeq stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,4481194200.0,29874628.0,RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:1207561849;C:1040055195;G:1022613796;T:1210492037;N:471323,75,75,,,1207561849,1040055195,1022613796,1210492037,471323,SRX7034691,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.92094,0.92157,0.07292,0.07281,0.74704,0.75067,0.47205,0.47416,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55395,SRR10323907,SRX7034690,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,16,16,TruSeq stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz,fastq fastq,2071385250.0,13809235.0,RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:497024628;C:535934066;G:538798491;T:499539772;N:88293,75,75,,,497024628,535934066,538798491,499539772,88293,SRX7034690,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.92507,0.92563,0.0745,0.07106,0.74148,0.74186,0.5137,0.52923,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55396,SRR10323908,SRX7034689,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,15,15,TruSeq stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,1708336800.0,11388912.0,RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:413739883;C:438115098;G:440441368;T:415968029;N:72422,75,75,,,413739883,438115098,440441368,415968029,72422,SRX7034689,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.92948,0.93123,0.08112,0.07757,0.7472,0.74921,0.49384,0.502,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55397,SRR10323909,SRX7034688,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2,14,14,TruSeq stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,2742841800.0,18285612.0,RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:771268784;C:600759252;G:605972112;T:764554978;N:286674,75,75,,,771268784,600759252,605972112,764554978,286674,SRX7034688,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.91195,0.91276,0.15552,0.15531,0.7191,0.7247,0.487,0.47379,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55398,SRR10323910,SRX7034687,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1,13,13,TruSeq stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,1909021350.0,12726809.0,RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:536542827;C:420010389;G:423642042;T:528630203;N:195889,75,75,,,536542827,420010389,423642042,528630203,195889,SRX7034687,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.91535,0.91534,0.11578,0.11457,0.73705,0.74373,0.47609,0.47115,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55399,SRR10323911,SRX7034686,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,12,12,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,5135290500.0,34235270.0,RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:1339180940;C:1202946694;G:1230552771;T:1362120185;N:489910,75,75,,,1339180940,1202946694,1230552771,1362120185,489910,SRX7034686,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.66031,0.70687,0.04575,0.04896,0.81075,0.81195,0.50951,0.47552,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55400,SRR10323912,SRX7034685,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,11,11,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,3890046300.0,25933642.0,RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:1020376762;C:903218301;G:916043426;T:1050047618;N:360193,75,75,,,1020376762,903218301,916043426,1050047618,360193,SRX7034685,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.70733,0.75223,0.05929,0.06271,0.80807,0.81071,0.48475,0.49323,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55401,SRR10323913,SRX7034684,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2,2,2,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz,fastq fastq,2547796350.0,16985309.0,RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz,0:75 1:75,A:686259539;C:560800822;G:567842650;T:732652800;N:240539,75,75,,,686259539,560800822,567842650,732652800,240539,SRX7034684,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.70188,0.75886,0.08072,0.08833,0.8034,0.80649,0.51507,0.5194,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System
55402,SRR10323914,SRX7034683,SRS5554730,SRP226614,PRJNA578896,Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence,PRJNA578896,Other,In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.,,,,,danRer10 raw data,,strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1,1,1,NEBNext Low Input RNA Library Prep Kit,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP226614,,,RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz,fastq fastq,2438070600.0,16253804.0,RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz,0:75 1:75,A:654282012;C:534555119;G:543878428;T:705130425;N:224616,75,75,,,654282012,534555119,543878428,705130425,224616,SRX7034683,SRS5554730,SRA983011,"Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology","Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany",2,0.69336,0.75626,0.09168,0.09896,0.80166,0.80253,0.51795,0.52538,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Germany,2019-10-24,Pharyngula,Embryo,Endothelium,Cardiovascular System