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49 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and tissue_curation = "Heart"

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devstage_curation_coarse 3

experiment.library_strategy 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Heart · 49 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • other · 49 ✖

experiment.library_layout 1

  • SINGLE · 49 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
50757 50757 SRR8305610 SRX5120156 SRS4121979 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   AgeCtr5Month#3   breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#3|BioSampleModel:Model organism or animal                 Healthy 5months rep3 miRNA 8990 8990 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8990_S16_L008_R1_001.fastq.gz fastq 698736950.0 13974739.0 SID8990 S16 L008 R1 001.fastq.gz 0:50 A:131989113;C:176394830;G:226656872;T:163673496;N:22639 50       131989113 176394830 226656872 163673496 22639 SRX5120156 SRS4121979 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00317   0.00059   0.99632   0.624   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50758 50758 SRR8305611 SRX5120155 SRS4121983 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   AgeCtr45dpi#2   breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#2|BioSampleModel:Model organism or animal                 AgeMatchCtr45dpi rep2 miRNA 8986 8986 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8986_S11_L007_R1_001.fastq.gz fastq 167880450.0 3357609.0 SID8986 S11 L007 R1 001.fastq.gz 0:50 A:31714312;C:42386139;G:55132141;T:38634835;N:13023 50       31714312 42386139 55132141 38634835 13023 SRX5120155 SRS4121983 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00595   0.00101   0.99685   0.70197   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50759 50759 SRR8305612 SRX5120154 SRS4121982 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   AgeCtr45dpi#3   breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#3|BioSampleModel:Model organism or animal                 AgeMatchCtr45dpi rep3 miRNA 8987 8987 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8987_S12_L007_R1_001.fastq.gz fastq 58209250.0 1164185.0 SID8987 S12 L007 R1 001.fastq.gz 0:50 A:11149995;C:14754333;G:18974261;T:13326125;N:4536 50       11149995 14754333 18974261 13326125 4536 SRX5120154 SRS4121982 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00501   0.00068   0.99778   0.66509   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50760 50760 SRR8305613 SRX5120153 SRS4121976 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   120dpi#2   breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#2|BioSampleModel:Model organism or animal                 120dpi rep2 miRNA 6025 6025 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6025_S29_L005_R1_001.fastq.gz fastq 920379950.0 18407599.0 SID6025 S29 L005 R1 001.fastq.gz 0:50 A:197341487;C:229231195;G:273629822;T:220038506;N:138940 50       197341487 229231195 273629822 220038506 138940 SRX5120153 SRS4121976 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01344   0.00253   0.99557   0.74965   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50761 50761 SRR8305614 SRX5120152 SRS4121978 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   120dpi#3   breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#3|BioSampleModel:Model organism or animal                 120dpi rep3 miRNA 6026 6026 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6026_S26_L005_R1_001.fastq.gz fastq 889209550.0 17784191.0 SID6026 S26 L005 R1 001.fastq.gz 0:50 A:185835825;C:227166683;G:267016163;T:209056255;N:134624 50       185835825 227166683 267016163 209056255 134624 SRX5120152 SRS4121978 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02108   0.00333   0.9945   0.72482   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50762 50762 SRR8305615 SRX5120151 SRS4121975 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   60dpi#3   breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#3|BioSampleModel:Model organism or animal                 60dpi rep3 miRNA 6023 6023 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6023_S25_L005_R1_001.fastq.gz fastq 807865300.0 16157306.0 SID6023 S25 L005 R1 001.fastq.gz 0:50 A:178927964;C:196404816;G:231871602;T:200541868;N:119050 50       178927964 196404816 231871602 200541868 119050 SRX5120151 SRS4121975 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01977   0.00475   0.99381   0.76643   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50763 50763 SRR8305616 SRX5120150 SRS4121977 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   120dpi#1   breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#1|BioSampleModel:Model organism or animal                 120dpi rep1 miRNA 6024 6024 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6024_S27_L005_R1_001.fastq.gz fastq 976958950.0 19539179.0 SID6024 S27 L005 R1 001.fastq.gz 0:50 A:207562906;C:245776777;G:289761611;T:233711355;N:146301 50       207562906 245776777 289761611 233711355 146301 SRX5120150 SRS4121977 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.024   0.00503   0.99415   0.68714   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50764 50764 SRR8305617 SRX5120149 SRS4121973 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   60dpi#1   breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#1|BioSampleModel:Model organism or animal                 60dpi rep1 miRNA 6021 6021 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6021_S30_L005_R1_001.fastq.gz fastq 822399250.0 16447985.0 SID6021 S30 L005 R1 001.fastq.gz 0:50 A:179285741;C:203624280;G:242490523;T:196874923;N:123783 50       179285741 203624280 242490523 196874923 123783 SRX5120149 SRS4121973 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00298   0.00065   0.99614   0.7096   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50765 50765 SRR8305618 SRX5120148 SRS4121974 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   60dpi#2   breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#2|BioSampleModel:Model organism or animal                 60dpi rep2 miRNA 6022 6022 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6022_S28_L005_R1_001.fastq.gz fastq 1185285550.0 23705711.0 SID6022 S28 L005 R1 001.fastq.gz 0:50 A:263566408;C:289358565;G:345225328;T:286957646;N:177603 50       263566408 289358565 345225328 286957646 177603 SRX5120148 SRS4121974 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00543   0.00143   0.99655   0.72969   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50766 50766 SRR8305619 SRX5120147 SRS4121969 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   45dpi#2   breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#2|BioSampleModel:Model organism or animal                 45dpi rep2 miRNA 6019 6019 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6019_S24_L004_R1_001.fastq.gz fastq 1665628850.0 33312577.0 SID6019 S24 L004 R1 001.fastq.gz 0:50 A:345040451;C:410823238;G:503499843;T:406069175;N:196143 50       345040451 410823238 503499843 406069175 196143 SRX5120147 SRS4121969 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01832   0.00329   0.99381   0.74442   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50767 50767 SRR8305620 SRX5120146 SRS4121972 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   45dpi#3   breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#3|BioSampleModel:Model organism or animal                 45dpi rep3 miRNA 6020 6020 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6020_S19_L004_R1_001.fastq.gz fastq 1077141150.0 21542823.0 SID6020 S19 L004 R1 001.fastq.gz 0:50 A:209184554;C:272965854;G:342027609;T:252836621;N:126512 50       209184554 272965854 342027609 252836621 126512 SRX5120146 SRS4121972 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02255   0.0041   0.9932   0.70804   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50768 50768 SRR8305621 SRX5120145 SRS4121971 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   30dpi#3   breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#3|BioSampleModel:Model organism or animal                 30dpi rep3 miRNA 6017 6017 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6017_S22_L004_R1_001.fastq.gz fastq 1471641150.0 29432823.0 SID6017 S22 L004 R1 001.fastq.gz 0:50 A:286808307;C:377070243;G:450396816;T:357191320;N:174464 50       286808307 377070243 450396816 357191320 174464 SRX5120145 SRS4121971 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00948   0.00145   0.99261   0.69419   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50769 50769 SRR8305622 SRX5120144 SRS4121970 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   45dpi#1   breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#1|BioSampleModel:Model organism or animal                 45dpi rep1 miRNA 6018 6018 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6018_S23_L004_R1_001.fastq.gz fastq 1354764100.0 27095282.0 SID6018 S23 L004 R1 001.fastq.gz 0:50 A:268591138;C:340728679;G:421161801;T:324122996;N:159486 50       268591138 340728679 421161801 324122996 159486 SRX5120144 SRS4121970 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.0221   0.00361   0.99371   0.69289   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50770 50770 SRR8305623 SRX5120143 SRS4121980 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   AgeCtr5Month#1   breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#1|BioSampleModel:Model organism or animal                 Healthy 5months rep1 miRNA 8988 8988 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8988_S14_L008_R1_001.fastq.gz fastq 55133800.0 1102676.0 SID8988 S14 L008 R1 001.fastq.gz 0:50 A:10235345;C:14001041;G:17872491;T:13023101;N:1822 50       10235345 14001041 17872491 13023101 1822 SRX5120143 SRS4121980 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01094   0.00175   0.98953   0.60545   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50771 50771 SRR8305624 SRX5120142 SRS4122008 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   1dpi#3   breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#3|BioSampleModel:Model organism or animal                 1dpi rep3 miRNA 6002 6002 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6002_S5_L001_R1_001.fastq.gz fastq 1578002200.0 31560044.0 SID6002 S5 L001 R1 001.fastq.gz 0:50 A:345828316;C:403094159;G:472136222;T:356835497;N:108006 50       345828316 403094159 472136222 356835497 108006 SRX5120142 SRS4122008 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.07196   0.01204   0.98628   0.6936   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50772 50772 SRR8305625 SRX5120141 SRS4122009 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   1dpi#2   breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#2|BioSampleModel:Model organism or animal                 1dpi rep2 miRNA 6001 6001 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6001_S4_L001_R1_001.fastq.gz fastq 1234803500.0 24696070.0 SID6001 S4 L001 R1 001.fastq.gz 0:50 A:251952768;C:310000103;G:374403246;T:298358838;N:88545 50       251952768 310000103 374403246 298358838 88545 SRX5120141 SRS4122009 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.05028   0.0095   0.98837   0.67564   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50773 50773 SRR8305626 SRX5120140 SRS4122010 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   4dpi#2   breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#2|BioSampleModel:Model organism or animal                 4dpi rep2 miRNA 6004 6004 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6004_S8_L002_R1_001.fastq.gz fastq 1250169750.0 25003395.0 SID6004 S8 L002 R1 001.fastq.gz 0:50 A:240593316;C:315540319;G:393819940;T:300120501;N:95674 50       240593316 315540319 393819940 300120501 95674 SRX5120140 SRS4122010 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02656   0.00415   0.99155   0.62344   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50774 50774 SRR8305627 SRX5120139 SRS4122011 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   4dpi#1   breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#1|BioSampleModel:Model organism or animal                 4dpi rep1 miRNA 6003 6003 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6003_S7_L002_R1_001.fastq.gz fastq 1563660750.0 31273215.0 SID6003 S7 L002 R1 001.fastq.gz 0:50 A:314953051;C:395817158;G:476754857;T:376018422;N:117262 50       314953051 395817158 476754857 376018422 117262 SRX5120139 SRS4122011 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.04092   0.00568   0.9895   0.69059   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50775 50775 SRR8305628 SRX5120138 SRS4122004 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   sham#2   breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#2|BioSampleModel:Model organism or animal                 sham rep2 miRNA 5998 5998 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID5998_S6_L001_R1_001.fastq.gz fastq 1588288100.0 31765762.0 SID5998 S6 L001 R1 001.fastq.gz 0:50 A:342796715;C:390105841;G:464467318;T:390803929;N:114297 50       342796715 390105841 464467318 390803929 114297 SRX5120138 SRS4122004 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.03765   0.00775   0.99371   0.71003   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50776 50776 SRR8305629 SRX5120137 SRS4122005 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   sham#1   breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#1|BioSampleModel:Model organism or animal                 sham rep1 miRNA 5997 5997 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID5997_S1_L005_R1_001.fastq.gz fastq 1551989700.0 31039794.0 SID5997 S1 L005 R1 001.fastq.gz 0:50 A:322274392;C:384135688;G:460825098;T:384698486;N:56036 50       322274392 384135688 460825098 384698486 56036 SRX5120137 SRS4122005 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.0173   0.00355   0.99571   0.71717   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50777 50777 SRR8305630 SRX5120136 SRS4122006 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   1dpi#1   breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#1|BioSampleModel:Model organism or animal                 1dpi rep1 miRNA 6000 6000 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6000_S3_L001_R1_001.fastq.gz fastq 1782388700.0 35647774.0 SID6000 S3 L001 R1 001.fastq.gz 0:50 A:346286113;C:454398380;G:577494456;T:404083801;N:125950 50       346286113 454398380 577494456 404083801 125950 SRX5120136 SRS4122006 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02786   0.00537   0.99103   0.80383   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50778 50778 SRR8305631 SRX5120135 SRS4122007 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   sham#3   breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#3|BioSampleModel:Model organism or animal                 sham rep3 miRNA 5999 5999 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID5999_S2_L001_R1_001.fastq.gz fastq 1062556900.0 21251138.0 SID5999 S2 L001 R1 001.fastq.gz 0:50 A:217053290;C:267053521;G:321242631;T:257131790;N:75668 50       217053290 267053521 321242631 257131790 75668 SRX5120135 SRS4122007 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01276   0.00266   0.99206   0.76992   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50779 50779 SRR8305632 SRX5120134 SRS4121981 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   AgeCtr5Month#2   breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#2|BioSampleModel:Model organism or animal                 Healthy 5months rep2 miRNA 8989 8989 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8989_S15_L008_R1_001.fastq.gz fastq 1238593550.0 24771871.0 SID8989 S15 L008 R1 001.fastq.gz 0:50 A:234342146;C:315041073;G:406169561;T:283000578;N:40192 50       234342146 315041073 406169561 283000578 40192 SRX5120134 SRS4121981 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.0018   0.00029   0.99707   0.75503   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50780 50780 SRR8305633 SRX5120133 SRS4122012 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   7dpi#1   breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#1|BioSampleModel:Model organism or animal                 7dpi rep1 miRNA 6006 6006 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6006_S10_L002_R1_001.fastq.gz fastq 2236210750.0 44724215.0 SID6006 S10 L002 R1 001.fastq.gz 0:50 A:418358075;C:559212196;G:698422326;T:560042907;N:175246 50       418358075 559212196 698422326 560042907 175246 SRX5120133 SRS4122012 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.03621   0.00542   0.99026   0.6579   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2018-12-13 Adult Adult Heart Cardiovascular System
50781 50781 SRR8305634 SRX5120132 SRS4122013 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   4dpi#3   breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#3|BioSampleModel:Model organism or animal                 4dpi rep3 miRNA 6005 6005 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6005_S9_L002_R1_001.fastq.gz fastq 1055547700.0 21110954.0 SID6005 S9 L002 R1 001.fastq.gz 0:50 A:206864874;C:267418316;G:328346657;T:252837721;N:80132 50       206864874 267418316 328346657 252837721 80132 SRX5120132 SRS4122013 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.03345   0.00484   0.99178   0.62838   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50782 50782 SRR8305635 SRX5120131 SRS4122001 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   AgeCtr45dpi#1   breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#1|BioSampleModel:Model organism or animal                 AgeMatchCtr45dpi rep1 miRNA 8985 8985 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8985_S10_L007_R1_001.fastq.gz fastq 157438950.0 3148779.0 SID8985 S10 L007 R1 001.fastq.gz 0:50 A:29907011;C:39967744;G:51803529;T:35747899;N:12767 50       29907011 39967744 51803529 35747899 12767 SRX5120131 SRS4122001 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00551   0.00091   0.99758   0.68992   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50783 50783 SRR8305636 SRX5120130 SRS4122003 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   AgeCtr120dpi#3   breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#3|BioSampleModel:Model organism or animal                 AgeMatchCtr120dpi rep3 miRNA 8984 8984 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8984_S8_L006_R1_001.fastq.gz fastq 527926150.0 10558523.0 SID8984 S8 L006 R1 001.fastq.gz 0:50 A:100249504;C:134536518;G:170369710;T:122751228;N:19190 50       100249504 134536518 170369710 122751228 19190 SRX5120130 SRS4122003 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00248   0.00046   0.99748   0.67021   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50784 50784 SRR8305637 SRX5120129 SRS4121987 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   AgeCtr160dpi#3   breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#3|BioSampleModel:Model organism or animal                 AgeMatchCtr160dpi rep3 miRNA 8981 8981 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8981_S4_L005_R1_001.fastq.gz fastq 461202550.0 9224051.0 SID8981 S4 L005 R1 001.fastq.gz 0:50 A:93413883;C:114608387;G:142367379;T:110796282;N:16619 50       93413883 114608387 142367379 110796282 16619 SRX5120129 SRS4121987 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01441   0.00274   0.99579   0.75424   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50785 50785 SRR8305638 SRX5120128 SRS4121989 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   AgeCtr160dpi#2   breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#2|BioSampleModel:Model organism or animal                 AgeMatchCtr160dpi rep2 miRNA 8980 8980 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8980_S3_L005_R1_001.fastq.gz fastq 709335250.0 14186705.0 SID8980 S3 L005 R1 001.fastq.gz 0:50 A:139628736;C:176770611;G:222154342;T:170755378;N:26183 50       139628736 176770611 222154342 170755378 26183 SRX5120128 SRS4121989 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01323   0.00258   0.99628   0.8087   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50786 50786 SRR8305639 SRX5120127 SRS4121984 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   AgeCtr120dpi#2   breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#2|BioSampleModel:Model organism or animal                 AgeMatchCtr120dpi rep2 miRNA 8983 8983 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8983_S7_L006_R1_001.fastq.gz fastq 110092850.0 2201857.0 SID8983 S7 L006 R1 001.fastq.gz 0:50 A:20832150;C:27890992;G:35337269;T:26028356;N:4083 50       20832150 27890992 35337269 26028356 4083 SRX5120127 SRS4121984 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00659   0.00124   0.99464   0.64092   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50787 50787 SRR8305640 SRX5120126 SRS4121985 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   AgeCtr120dpi#1   breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#1|BioSampleModel:Model organism or animal                 AgeMatchCtr120dpi rep1 miRNA 8982 8982 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8982_S6_L006_R1_001.fastq.gz fastq 274783000.0 5495660.0 SID8982 S6 L006 R1 001.fastq.gz 0:50 A:51202860;C:70356196;G:89068979;T:64144960;N:10005 50       51202860 70356196 89068979 64144960 10005 SRX5120126 SRS4121985 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00736   0.00142   0.99519   0.67978   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50788 50788 SRR8305641 SRX5120125 SRS4121991 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   160dpi#2   breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#2|BioSampleModel:Model organism or animal                 160dpi rep2 miRNA 7273 7273 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID7273_S13_L008_R1_001.fastq.gz fastq 1562494050.0 31249881.0 SID7273 S13 L008 R1 001.fastq.gz 0:50 A:322066209;C:401076329;G:458040591;T:381260838;N:50083 50       322066209 401076329 458040591 381260838 50083 SRX5120125 SRS4121991 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.00546   0.00063   0.99758   0.63443   50   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50789 50789 SRR8305642 SRX5120124 SRS4121992 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   160dpi#1   breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#1|BioSampleModel:Model organism or animal                 160dpi rep1 miRNA 6754 6754 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6754_S12_L002_R1_001.fastq.gz fastq 970614525.0 12941527.0 SID6754 S12 L002 R1 001.fastq.gz 0:75 A:226197330;C:263276797;G:244870748;T:236180457;N:89193 75       226197330 263276797 244870748 236180457 89193 SRX5120124 SRS4121992 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 6e-05   1e-05   0.99985   0.75   75   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50790 50790 SRR8305643 SRX5120123 SRS4121993 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   AgeCtr160dpi#1   breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#1|BioSampleModel:Model organism or animal                 AgeMatchCtr160dpi rep1 miRNA 8979 8979 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID8979_S2_L005_R1_001.fastq.gz fastq 1191571700.0 23831434.0 SID8979 S2 L005 R1 001.fastq.gz 0:50 A:231936155;C:298463393;G:377425675;T:283702936;N:43541 50       231936155 298463393 377425675 283702936 43541 SRX5120123 SRS4121993 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.01636   0.00334   0.99478   0.78529   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50791 50791 SRR8305644 SRX5120122 SRS4121990 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   160dpi#3   breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#3|BioSampleModel:Model organism or animal                 160dpi rep3 miRNA 7274 7274 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID7274_S18_L003_R1_001.fastq.gz fastq 587672100.0 7835628.0 SID7274 S18 L003 R1 001.fastq.gz 0:75 A:128228313;C:152211828;G:156460760;T:150725049;N:46150 75       128228313 152211828 156460760 150725049 46150 SRX5120122 SRS4121990 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 9e-05   1e-05   0.99975   0.46153   75   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50792 50792 SRR8305645 SRX5120121 SRS4122000 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   21dpi#3   breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#3|BioSampleModel:Model organism or animal                 21dpi rep3 miRNA 6014 6014 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6014_S18_L003_R1_001.fastq.gz fastq 470984100.0 9419682.0 SID6014 S18 L003 R1 001.fastq.gz 0:50 A:90590892;C:122988758;G:143456400;T:113917917;N:30133 50       90590892 122988758 143456400 113917917 30133 SRX5120121 SRS4122000 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02203   0.00201   0.99312   0.39653   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2018-12-13 Adult Adult Heart Cardiovascular System
50793 50793 SRR8305646 SRX5120120 SRS4122002 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   21dpi#2   breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#2|BioSampleModel:Model organism or animal                 21dpi rep2 miRNA 6013 6013 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6013_S17_L003_R1_001.fastq.gz fastq 785630400.0 15712608.0 SID6013 S17 L003 R1 001.fastq.gz 0:50 A:152017861;C:201679585;G:240972325;T:190910430;N:50199 50       152017861 201679585 240972325 190910430 50199 SRX5120120 SRS4122002 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02519   0.00378   0.99373   0.40787   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50794 50794 SRR8305647 SRX5120119 SRS4121999 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   21dpi#1   breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#1|BioSampleModel:Model organism or animal                 21dpi rep1 miRNA 6012 6012 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6012_S16_L003_R1_001.fastq.gz fastq 494552600.0 9891052.0 SID6012 S16 L003 R1 001.fastq.gz 0:50 A:95336093;C:129024365;G:149497515;T:120663807;N:30820 50       95336093 129024365 149497515 120663807 30820 SRX5120119 SRS4121999 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.04208   0.00538   0.992   0.61501   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50795 50795 SRR8305648 SRX5120118 SRS4121998 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   14dpi#3   breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#3|BioSampleModel:Model organism or animal                 14dpi rep3 miRNA 6011 6011 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6011_S15_L003_R1_001.fastq.gz fastq 578164050.0 11563281.0 SID6011 S15 L003 R1 001.fastq.gz 0:50 A:109934197;C:149003532;G:179264553;T:139924815;N:36953 50       109934197 149003532 179264553 139924815 36953 SRX5120118 SRS4121998 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.0225   0.00372   0.9906   0.61747   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Undetermined Undetermined Heart Cardiovascular System
50796 50796 SRR8305649 SRX5120117 SRS4121996 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   14dpi#2   breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#2|BioSampleModel:Model organism or animal                 14dpi rep2 miRNA 6010 6010 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6010_S14_L003_R1_001.fastq.gz fastq 682820200.0 13656404.0 SID6010 S14 L003 R1 001.fastq.gz 0:50 A:132413613;C:177691857;G:213067602;T:159602931;N:44197 50       132413613 177691857 213067602 159602931 44197 SRX5120117 SRS4121996 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02361   0.00321   0.99281   0.46548   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Undetermined Undetermined Heart Cardiovascular System
50797 50797 SRR8305650 SRX5120116 SRS4121997 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   14dpi#1   breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#1|BioSampleModel:Model organism or animal                 14dpi rep1 miRNA 6009 6009 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6009_S5_L006_R1_001.fastq.gz fastq 645018650.0 12900373.0 SID6009 S5 L006 R1 001.fastq.gz 0:50 A:121217579;C:170403284;G:199790376;T:153583951;N:23460 50       121217579 170403284 199790376 153583951 23460 SRX5120116 SRS4121997 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.02637   0.00359   0.99095   0.50364   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Undetermined Undetermined Heart Cardiovascular System
50798 50798 SRR8305651 SRX5120115 SRS4121994 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 3   7dpi#3   breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#3|BioSampleModel:Model organism or animal                 7dpi rep3 miRNA 6008 6008 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6008_S11_L002_R1_001.fastq.gz fastq 1016249900.0 20324998.0 SID6008 S11 L002 R1 001.fastq.gz 0:50 A:196023277;C:256234305;G:315577111;T:248336546;N:78661 50       196023277 256234305 315577111 248336546 78661 SRX5120115 SRS4121994 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.03415   0.00416   0.98981   0.66977   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50799 50799 SRR8305652 SRX5120114 SRS4121995 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   7dpi#2   breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#2|BioSampleModel:Model organism or animal                 7dpi rep2 miRNA 6007 6007 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6007_S12_L002_R1_001.fastq.gz fastq 1405772250.0 28115445.0 SID6007 S12 L002 R1 001.fastq.gz 0:50 A:270753665;C:356955121;G:444759435;T:333191995;N:112034 50       270753665 356955121 444759435 333191995 112034 SRX5120114 SRS4121995 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.0195   0.00225   0.99291   0.65233   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2018-12-13 Adult Adult Heart Cardiovascular System
50800 50800 SRR8305653 SRX5120113 SRS4121986 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 2   30dpi#2   breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#2|BioSampleModel:Model organism or animal                 30dpi rep2 miRNA 6016 6016 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6016_S21_L004_R1_001.fastq.gz fastq 1317403300.0 26348066.0 SID6016 S21 L004 R1 001.fastq.gz 0:50 A:248382887;C:331301718;G:402502543;T:335061139;N:155013 50       248382887 331301718 402502543 335061139 155013 SRX5120113 SRS4121986 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.05594   0.00908   0.98569   0.68185   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
50801 50801 SRR8305654 SRX5120112 SRS4121988 SRP173044 PRJNA509429 Delineating the transcriptomic response during Zebrafish heart regeneration PRJNA509429 Other Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.   pubmed:30597924 Replicate 1   30dpi#1   breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#1|BioSampleModel:Model organism or animal                 30dpi rep1 miRNA 6015 6015 miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613     miRNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP173044     SID6015_S20_L004_R1_001.fastq.gz fastq 1342409800.0 26848196.0 SID6015 S20 L004 R1 001.fastq.gz 0:50 A:256149333;C:337592303;G:419179623;T:329329916;N:158625 50       256149333 337592303 419179623 329329916 158625 SRX5120112 SRS4121988 SRA822004 University of Freiburg|Institute of Molecular Medicine and Cell Research University of Freiburg DeCaRe 1 0.03123   0.00479   0.98999   0.62344   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   Germany 2019-04-30 Adult Adult Heart Cardiovascular System
71064 71064 SRR21218373 SRX17229104 SRS14795570 SRP394145 PRJNA872137 The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration. GSE211793 Other The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.   pubmed:37306388   zebrafish Ribo seq Eif4e1c / rep2 [r mR2] GSM6502516   source name:heart|tissue:heart|cell line:Mutant|genotype:Eif4e1c / zebrafish Ribo seq Eif4e1c / rep2 [r mR2] Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq heart   The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3 Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity. tissue:heart|cell line:Mutant|genotype:Eif4e1c / GSM6502516 GSM6502516: zebrafish Ribo seq Eif4e1c / rep2 [r mR2]; Danio rerio; OTHER GSM6502516 r1 GSM6502516 1 The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 550   SRP394145     rS4_mR2.fastq.gz fastq 6611131472.0 86988572.0 GSM6502516 r1 0:76 1:0 A:1748359123;C:1658689534;G:1706027528;T:1497702781;N:352506 76 0     1748359123 1658689534 1706027528 1497702781 352506 SRX17229104 SRS14795570 SRA1485233 Biological Chemistry and Pharmacology, The Ohio State University Biological Chemistry and Pharmacology, The Ohio State University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   United States 2022-08-22 Undetermined Multi-stage Heart Cardiovascular System
71065 71065 SRR21218374 SRX17229103 SRS14795569 SRP394145 PRJNA872137 The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration. GSE211793 Other The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.   pubmed:37306388   zebrafish Ribo seq Eif4e1c / rep 1 [r mR1] GSM6502515   source name:heart|tissue:heart|cell line:Mutant|genotype:Eif4e1c / zebrafish Ribo seq Eif4e1c / rep 1 [r mR1] Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq heart   The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3 Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity. tissue:heart|cell line:Mutant|genotype:Eif4e1c / GSM6502515 GSM6502515: zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]; Danio rerio; OTHER GSM6502515 r1 GSM6502515 1 The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 550   SRP394145     rS3_mR1.fastq.gz fastq 13677356644.0 179965219.0 GSM6502515 r1 0:76 1:0 A:3346749848;C:3412648254;G:3629003006;T:3288222747;N:732789 76 0     3346749848 3412648254 3629003006 3288222747 732789 SRX17229103 SRS14795569 SRA1485233 Biological Chemistry and Pharmacology, The Ohio State University Biological Chemistry and Pharmacology, The Ohio State University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   United States 2022-08-22 Undetermined Multi-stage Heart Cardiovascular System
71066 71066 SRR21218377 SRX17229102 SRS14795568 SRP394145 PRJNA872137 The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration. GSE211793 Other The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.   pubmed:37306388   zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2] GSM6502514   source name:heart|tissue:heart|cell line:Wt|genotype:Eif4e1c +/+ zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2] Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq heart   The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3 Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity. tissue:heart|cell line:Wt|genotype:Eif4e1c +/+ GSM6502514 GSM6502514: zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]; Danio rerio; OTHER GSM6502514 r1 GSM6502514 1 The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 550   SRP394145     rS2_pR2.fastq.gz fastq 8919983048.0 117368198.0 GSM6502514 r1 0:76 1:0 A:2208663451;C:2257902067;G:2371468879;T:2081476473;N:472178 76 0     2208663451 2257902067 2371468879 2081476473 472178 SRX17229102 SRS14795568 SRA1485233 Biological Chemistry and Pharmacology, The Ohio State University Biological Chemistry and Pharmacology, The Ohio State University 1 1e-05   0.0   0.99997   1.0   76   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   United States 2022-08-22 Undetermined Multi-stage Heart Cardiovascular System
71067 71067 SRR21218378 SRX17229101 SRS14795567 SRP394145 PRJNA872137 The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration. GSE211793 Other The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.   pubmed:37306388   zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1] GSM6502513   source name:heart|tissue:heart|cell line:Wt|genotype:Eif4e1c +/+ zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1] Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq heart   The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3 Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity. tissue:heart|cell line:Wt|genotype:Eif4e1c +/+ GSM6502513 GSM6502513: zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]; Danio rerio; OTHER GSM6502513 r1 GSM6502513 1 The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 550   SRP394145     rS1_pR1.fastq.gz fastq 8551941876.0 112525551.0 GSM6502513 r1 0:76 1:0 A:2015417703;C:2191682962;G:2364697448;T:1979683824;N:459939 76 0     2015417703 2191682962 2364697448 1979683824 459939 SRX17229101 SRS14795567 SRA1485233 Biological Chemistry and Pharmacology, The Ohio State University Biological Chemistry and Pharmacology, The Ohio State University 1 1e-05   0.0   0.99997   0.0   76   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   United States 2022-08-22 Undetermined Multi-stage Heart Cardiovascular System

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