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739 rows where experiment.library_selection = "size fractionation" and experiment.library_source = "TRANSCRIPTOMIC"

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tissue_curation >10

devstage_curation >10

devstage_curation_coarse 6

technology 4

experiment.platform 4

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experiment.library_layout 2

experiment.library_source 1

  • TRANSCRIPTOMIC · 739 ✖

experiment.library_selection 1

  • size fractionation · 739 ✖
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
15081 15081 ERR12476478 ERX11852299 ERS17743543 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242D Starved 1242SD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:201 277053 1242SD 1     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SD_S14_L003_R1_001.fastq.gz fastq 95457398.0 1268859.0 ena RUN TAB 15 01 2024 21:42:36:202 277054 0:75.23 A:33339157;C:18598733;G:20350072;T:23148005;N:21431 75       33339157 18598733 20350072 23148005 21431 ERX11852299 ERS17743543 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown size_fractionation unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
25162 25162 SRR25655085 SRX21381122 SRS18622091 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 8 AU1038 STRSS4 GSM7712891   source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing Sample 8 AU1038 STRSS4 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:From parent chronically stressed GSM7712891 GSM7712891: Sample 8 AU1038 STRSS4; Danio rerio; ncRNA Seq GSM7712891 r1 GSM7712891 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py STRS04_10932AAD_TGTCCTAC-ACATGAGT_R1_001.fastq.gz fastq 641236400.0 12824728.0 GSM7712891 r1 0:50 A:183546979;C:159774155;G:156033079;T:141881902;N:285 50       183546979 159774155 156033079 141881902 285 SRX21381122 SRS18622091 SRA1693666 CNAG CNAG 1 0.4736   0.03992   0.96788   0.87662   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25163 25163 SRR25655086 SRX21381121 SRS18622090 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 7 AU1037 STRSS3 GSM7712890   source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing Sample 7 AU1037 STRSS3 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:From parent chronically stressed GSM7712890 GSM7712890: Sample 7 AU1037 STRSS3; Danio rerio; ncRNA Seq GSM7712890 r1 GSM7712890 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py STRS03_10931AAD_GCACGATT-CGTCTGCA_R1_001.fastq.gz fastq 434646850.0 8692937.0 GSM7712890 r1 0:50 A:126760670;C:102577685;G:109591447;T:95716876;N:172 50       126760670 102577685 109591447 95716876 172 SRX21381121 SRS18622090 SRA1693666 CNAG CNAG 1 0.52132   0.04615   0.96477   0.85481   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25164 25164 SRR25655087 SRX21381120 SRS18622089 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 6 AU1036 STRSS2 GSM7712889   source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing Sample 6 AU1036 STRSS2 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:From parent chronically stressed GSM7712889 GSM7712889: Sample 6 AU1036 STRSS2; Danio rerio; ncRNA Seq GSM7712889 r1 GSM7712889 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py STRS02_10930AAD_ATGAAGCG-GCGGACAG_R1_001.fastq.gz fastq 907610650.0 18152213.0 GSM7712889 r1 0:50 A:271494673;C:215304417;G:220608756;T:200202267;N:537 50       271494673 215304417 220608756 200202267 537 SRX21381120 SRS18622089 SRA1693666 CNAG CNAG 1 0.44189   0.03477   0.97335   0.88092   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25165 25165 SRR25655088 SRX21381119 SRS18622088 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 5 AU1035 STRSS1 GSM7712888   source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing Sample 5 AU1035 STRSS1 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:From parent chronically stressed GSM7712888 GSM7712888: Sample 5 AU1035 STRSS1; Danio rerio; ncRNA Seq GSM7712888 r1 GSM7712888 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py STRS01_10929AAD_CACTTCGA-TAGGCTTC_R1_001.fastq.gz fastq 711276100.0 14225522.0 GSM7712888 r1 0:50 A:207284968;C:173540770;G:172961619;T:157488473;N:270 50       207284968 173540770 172961619 157488473 270 SRX21381119 SRS18622088 SRA1693666 CNAG CNAG 1 0.47865   0.03881   0.97001   0.87616   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25166 25166 SRR25655089 SRX21381118 SRS18622087 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 4 AU1028 CTRL4 GSM7712887   source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing Sample 4 AU1028 CTRL4 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:Control GSM7712887 GSM7712887: Sample 4 AU1028 CTRL4; Danio rerio; ncRNA Seq GSM7712887 r1 GSM7712887 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py CTRL04_10928AAD_GACTAGGC-GCCTCGAC_R1_001.fastq.gz fastq 568037350.0 11360747.0 GSM7712887 r1 0:50 A:165826590;C:133109854;G:141956673;T:127143732;N:501 50       165826590 133109854 141956673 127143732 501 SRX21381118 SRS18622087 SRA1693666 CNAG CNAG 1 0.48051   0.0347   0.97268   0.87465   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25167 25167 SRR25655090 SRX21381117 SRS18622086 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 3 AU1027 CTRL3 GSM7712886   source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing Sample 3 AU1027 CTRL3 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:Control GSM7712886 GSM7712886: Sample 3 AU1027 CTRL3; Danio rerio; ncRNA Seq GSM7712886 r1 GSM7712886 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py CTRL03_10927AAD_AGTATACT-CGAATCGG_R1_001.fastq.gz fastq 651469300.0 13029386.0 GSM7712886 r1 0:50 A:191788726;C:154951271;G:161329211;T:143399936;N:156 50       191788726 154951271 161329211 143399936 156 SRX21381117 SRS18622086 SRA1693666 CNAG CNAG 1 0.45412   0.04073   0.96934   0.88507   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25168 25168 SRR25655091 SRX21381116 SRS18622085 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 2 AU1026 CTRL2 GSM7712885   source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing Sample 2 AU1026 CTRL2 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:Control GSM7712885 GSM7712885: Sample 2 AU1026 CTRL2; Danio rerio; ncRNA Seq GSM7712885 r1 GSM7712885 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py CTRL02_10926AAD_CCGCGTAG-TTCTGATT_R1_001.fastq.gz fastq 754615100.0 15092302.0 GSM7712885 r1 0:50 A:217013981;C:184328493;G:188964773;T:164307508;N:345 50       217013981 184328493 188964773 164307508 345 SRX21381116 SRS18622085 SRA1693666 CNAG CNAG 1 0.48926   0.04654   0.96418   0.8889   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25169 25169 SRR25655092 SRX21381115 SRS18622084 SRP455342 PRJNA1005926 miR 29a is downregulated in progenies derived from chronically stressed males GSE240954 Transcriptome Analysis To investigate the potential vertical transmission of chronic stress to the unexposed larvae to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.   pubmed:37762407   Sample 1 AU1024 CTRL1 GSM7712884   source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing Sample 1 AU1024 CTRL1 Trimming with trim galore v0.6.6 length 16 stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts larvae   RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   tissue:larvae|genotype:WT|treatment:Control GSM7712884 GSM7712884: Sample 1 AU1024 CTRL1; Danio rerio; ncRNA Seq GSM7712884 r1 GSM7712884 1 RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP455342   loader:fastq load.py CTRL01_10925AAD_TTAGCCTA-AATCATCA_R1_001.fastq.gz fastq 670580700.0 13411614.0 GSM7712884 r1 0:50 A:194653643;C:158916446;G:165941477;T:151068917;N:217 50       194653643 158916446 165941477 151068917 217 SRX21381115 SRS18622084 SRA1693666 CNAG CNAG 1 0.47093   0.03457   0.97187   0.8867   50   B   usable mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2023-08-16 Larval Larval Undetermined Undetermined
25277 25277 SRR30160454 SRX25627658 SRS22272474 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf charged tRNA seqrep 3 GSM8441306   tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing WT bud 10 hpf charged tRNA seqrep 3 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions 10 hpf embryos   Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   cell type:10 hpf embryos GSM8441306 GSM8441306: WT bud 10 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq GSM8441306 r1 GSM8441306 1 Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457111     10hpf_aa_rep3.fastq.gz fastq 193965330.0 3367323.0 GSM8441306 r1 0:57.60 A:36799299;C:55100074;G:53758955;T:48306966;N:36 57       36799299 55100074 53758955 48306966 36 SRX25627658 SRS22272474 SRA1941998 Max Planck Institute of Biochemistry Max Planck Institute of Biochemistry 1 0.34405   0.05049   0.89471   0.46469   88   B   usable mapping rate illumina novaseq_era 5prime size_fractionation unknown bulk unknown unknown   Germany 2024-08-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
25278 25278 SRR30160455 SRX25627657 SRS22272473 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf charged tRNA seqrep 2 GSM8441305   tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing WT bud 10 hpf charged tRNA seqrep 2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions 10 hpf embryos   Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   cell type:10 hpf embryos GSM8441305 GSM8441305: WT bud 10 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq GSM8441305 r1 GSM8441305 1 Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457111     10hpf_aa_rep2.fastq.gz fastq 138524715.0 2369009.0 GSM8441305 r1 0:58.47 A:26396279;C:39139297;G:38459048;T:34530060;N:31 58       26396279 39139297 38459048 34530060 31 SRX25627657 SRS22272473 SRA1941998 Max Planck Institute of Biochemistry Max Planck Institute of Biochemistry 1 0.35458   0.05179   0.89424   0.46401   74   B   usable mapping rate illumina novaseq_era 5prime size_fractionation unknown bulk unknown unknown   Germany 2024-08-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
25279 25279 SRR30160456 SRX25627656 SRS22272472 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf charged tRNA seqrep 1 GSM8441304   tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing WT bud 10 hpf charged tRNA seqrep 1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions 10 hpf embryos   Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   cell type:10 hpf embryos GSM8441304 GSM8441304: WT bud 10 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq GSM8441304 r1 GSM8441304 1 Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457111     10hpf_aa_rep1.fastq.gz fastq 54473618.0 946419.0 GSM8441304 r1 0:57.56 A:10345022;C:15413782;G:15135500;T:13579304;N:10 57       10345022 15413782 15135500 13579304 10 SRX25627656 SRS22272472 SRA1941998 Max Planck Institute of Biochemistry Max Planck Institute of Biochemistry 1 0.36103   0.0515   0.89227   0.4748   81   B   usable mapping rate illumina novaseq_era 5prime size_fractionation unknown bulk unknown unknown   Germany 2024-08-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
25280 25280 SRR30160457 SRX25627655 SRS22272471 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf charged tRNA seqrep 3 GSM8441303   tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing WT sphere 4 hpf charged tRNA seqrep 3 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions 4 hpf embryos   Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   cell type:4 hpf embryos GSM8441303 GSM8441303: WT sphere 4 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq GSM8441303 r1 GSM8441303 1 Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457111     4hpf_aa_rep3.fastq.gz fastq 100810543.0 1747597.0 GSM8441303 r1 0:57.69 A:20466558;C:28054923;G:26849246;T:25439798;N:18 57       20466558 28054923 26849246 25439798 18 SRX25627655 SRS22272471 SRA1941998 Max Planck Institute of Biochemistry Max Planck Institute of Biochemistry 1 0.36374   0.06294   0.87316   0.54642   39   B   usable mapping rate illumina novaseq_era 5prime size_fractionation unknown bulk unknown unknown   Germany 2024-08-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
25281 25281 SRR30160458 SRX25627654 SRS22272470 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf charged tRNA seqrep 2 GSM8441302   tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing WT sphere 4 hpf charged tRNA seqrep 2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions 4 hpf embryos   Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   cell type:4 hpf embryos GSM8441302 GSM8441302: WT sphere 4 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq GSM8441302 r1 GSM8441302 1 Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457111     4hpf_aa_rep2.fastq.gz fastq 121662759.0 2046536.0 GSM8441302 r1 0:59.45 A:24519095;C:33689156;G:32726095;T:30728382;N:31 59       24519095 33689156 32726095 30728382 31 SRX25627654 SRS22272470 SRA1941998 Max Planck Institute of Biochemistry Max Planck Institute of Biochemistry 1 0.3726   0.06263   0.87136   0.55584   31   B   usable mapping rate illumina novaseq_era 5prime size_fractionation unknown bulk unknown unknown   Germany 2024-08-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
25282 25282 SRR30160459 SRX25627653 SRS22272469 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf charged tRNA seqrep 1 GSM8441301   tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing WT sphere 4 hpf charged tRNA seqrep 1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions 4 hpf embryos   Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   cell type:4 hpf embryos GSM8441301 GSM8441301: WT sphere 4 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq GSM8441301 r1 GSM8441301 1 Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457111     4hpf_aa_rep1.fastq.gz fastq 124990980.0 2116213.0 GSM8441301 r1 0:59.06 A:25487542;C:34621140;G:33284460;T:31597816;N:22 59       25487542 34621140 33284460 31597816 22 SRX25627653 SRS22272469 SRA1941998 Max Planck Institute of Biochemistry Max Planck Institute of Biochemistry 1 0.36013   0.05967   0.87387   0.55002   44   B   usable mapping rate illumina novaseq_era 5prime size_fractionation unknown bulk unknown unknown   Germany 2024-08-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
25283 25283 SRR25764121 SRX21486801 SRS18719093 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf tRNA seq rep2 GSM7734782   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing WT bud 10 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT GSM7734782 GSM7734782: WT bud 10 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734782 r1 GSM7734782 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_bud_2.fastq.gz fastq 278145656.0 4215107.0 GSM7734782 r1 0:65.99 A:52499947;C:77161357;G:79314034;T:69169753;N:565 65       52499947 77161357 79314034 69169753 565 SRX21486801 SRS18719093 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.31888   0.01661   0.92348   0.40156   75   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25284 25284 SRR25764122 SRX21486800 SRS18719092 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf tRNA seq rep1 GSM7734781   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing WT bud 10 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT GSM7734781 GSM7734781: WT bud 10 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734781 r1 GSM7734781 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_bud_1.fastq.gz fastq 385514625.0 5770392.0 GSM7734781 r1 0:66.81 A:73305393;C:107155246;G:109793285;T:95259823;N:878 66       73305393 107155246 109793285 95259823 878 SRX21486800 SRS18719092 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.33213   0.01782   0.92354   0.42724   39   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25285 25285 SRR25764123 SRX21486799 SRS18719098 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT shield 6 hpf tRNA seq rep2 GSM7734780   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT|geo loc name:missing|collection date:missing WT shield 6 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT GSM7734780 GSM7734780: WT shield 6 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734780 r1 GSM7734780 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_shield_2.fastq.gz fastq 469031736.0 7421688.0 GSM7734780 r1 0:63.20 A:90257219;C:130440728;G:130549302;T:117783411;N:1076 63       90257219 130440728 130549302 117783411 1076 SRX21486799 SRS18719098 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.29535   0.02113   0.91528   0.43824   37   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25286 25286 SRR25764124 SRX21486798 SRS18719100 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT shield 6 hpf tRNA seq rep1 GSM7734779   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT|geo loc name:missing|collection date:missing WT shield 6 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT GSM7734779 GSM7734779: WT shield 6 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734779 r1 GSM7734779 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_shield_1.fastq.gz fastq 487207771.0 7521930.0 GSM7734779 r1 0:64.77 A:94654510;C:134893975;G:135716906;T:121941280;N:1100 64       94654510 134893975 135716906 121941280 1100 SRX21486798 SRS18719100 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.30664   0.02274   0.91297   0.46012   79   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25287 25287 SRR25764125 SRX21486797 SRS18719094 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf tRNA seq rep2 GSM7734778   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing WT sphere 4 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT GSM7734778 GSM7734778: WT sphere 4 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734778 r1 GSM7734778 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_sphere_2.fastq.gz fastq 196089572.0 2998867.0 GSM7734778 r1 0:65.39 A:39134451;C:53803100;G:53602781;T:49548779;N:461 65       39134451 53803100 53602781 49548779 461 SRX21486797 SRS18719094 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.28808   0.01959   0.91553   0.47742   78   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25288 25288 SRR25764126 SRX21486796 SRS18719096 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf tRNA seq rep1 GSM7734777   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing WT sphere 4 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT GSM7734777 GSM7734777: WT sphere 4 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734777 r1 GSM7734777 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_sphere_1.fastq.gz fastq 273027894.0 4080366.0 GSM7734777 r1 0:66.91 A:54678043;C:74713512;G:74872888;T:68762883;N:568 66       54678043 74713512 74872888 68762883 568 SRX21486796 SRS18719096 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.30124   0.01877   0.9163   0.49987   79   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25289 25289 SRR25764127 SRX21486795 SRS18719097 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT 1000 cell 3 hpf tRNA seq rep2 GSM7734776   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT|geo loc name:missing|collection date:missing WT 1000 cell 3 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT GSM7734776 GSM7734776: WT 1000 cell 3 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734776 r1 GSM7734776 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_1Kcell_2.fastq.gz fastq 240973473.0 3918764.0 GSM7734776 r1 0:61.49 A:48091658;C:66684510;G:65183534;T:61013184;N:587 61       48091658 66684510 65183534 61013184 587 SRX21486795 SRS18719097 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.26629   0.02297   0.92305   0.48525   79   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25290 25290 SRR25764128 SRX21486794 SRS18719095 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT 1000 cell 3 hpf tRNA seq rep1 GSM7734775   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT|geo loc name:missing|collection date:missing WT 1000 cell 3 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT GSM7734775 GSM7734775: WT 1000 cell 3 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734775 r1 GSM7734775 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_1Kcell_1.fastq.gz fastq 153597915.0 2445091.0 GSM7734775 r1 0:62.82 A:30905842;C:42377268;G:41639937;T:38674503;N:365 62       30905842 42377268 41639937 38674503 365 SRX21486794 SRS18719095 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.27317   0.02516   0.92454   0.49385   77   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25291 25291 SRR25764129 SRX21486793 SRS18719091 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT 256 cell 2.5 hpf tRNA seq rep2 GSM7734774   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT|geo loc name:missing|collection date:missing WT 256 cell 2.5 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT GSM7734774 GSM7734774: WT 256 cell 2.5 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734774 r1 GSM7734774 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_256cell_2.fastq.gz fastq 844659062.0 13660310.0 GSM7734774 r1 0:61.83 A:165996817;C:234451560;G:230230791;T:213977958;N:1936 61       165996817 234451560 230230791 213977958 1936 SRX21486793 SRS18719091 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.26001   0.01993   0.92594   0.45714   61   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25292 25292 SRR25764130 SRX21486792 SRS18719088 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT 256 cell 2.5 hpf tRNA seq rep1 GSM7734773   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT|geo loc name:missing|collection date:missing WT 256 cell 2.5 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT GSM7734773 GSM7734773: WT 256 cell 2.5 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734773 r1 GSM7734773 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_256cell_1.fastq.gz fastq 215968508.0 3436266.0 GSM7734773 r1 0:62.85 A:43791388;C:59547637;G:58130851;T:54498124;N:508 62       43791388 59547637 58130851 54498124 508 SRX21486792 SRS18719088 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.27383   0.02205   0.92748   0.46217   71   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25293 25293 SRR25764131 SRX21486791 SRS18719090 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT egg 0 hpf tRNA seq rep2 GSM7734772   source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing WT egg 0 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Unfertilized egg unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT GSM7734772 GSM7734772: WT egg 0 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734772 r1 GSM7734772 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_egg_2.fastq.gz fastq 206374994.0 3181706.0 GSM7734772 r1 0:64.86 A:41195250;C:56578032;G:56479855;T:52121365;N:492 64       41195250 56578032 56479855 52121365 492 SRX21486791 SRS18719090 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.28659   0.02017   0.9207   0.48536   78   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Zygote Embryo Oocyte Reproductive System
25294 25294 SRR25764132 SRX21486790 SRS18719089 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT egg 0 hpf tRNA seq rep1 GSM7734771   source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing WT egg 0 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Unfertilized egg unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT GSM7734771 GSM7734771: WT egg 0 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734771 r1 GSM7734771 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_egg_1.fastq.gz fastq 86021968.0 1304769.0 GSM7734771 r1 0:65.93 A:17511521;C:23474625;G:23300759;T:21734864;N:199 65       17511521 23474625 23300759 21734864 199 SRX21486790 SRS18719089 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.29829   0.02027   0.92245   0.48877   74   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Zygote Embryo Oocyte Reproductive System
28490 28490 SRR26319601 SRX22027740 SRS19100857 SRP465070 PRJNA1025141 Danio rerio Raw sequence reads PRJNA1025141 Other Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.     Treatment CX3 for transcriptome 3 CX3   strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.67 E|treatment:Treatment Group|BioSampleModel:Model organism or animal                 ALST3 for transcriptome 3 CX3 for transcriptome 3 CX3 for transcriptome 3 CX3 for transcriptome 3     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Ten   SRP465070     Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz fastq fastq 6255596356.0 20929531.0 Unknown AY803 03T0006 good 1.fq.gz 0:149.44 1:149.44 A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506 149 149     1657365560 1463722268 1467057724 1667269298 181506 SRX22027740 SRS19100857 SRA1727563 Soochow University|School of biology & basic medical sciences Soochow University 2 0.89228 0.91654 0.09286 0.09714 0.6588 0.65604 0.4631 0.45773 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2023-10-11 Larval Larval Whole Organism All anatomical structures
28491 28491 SRR26319602 SRX22027739 SRS19100854 SRP465070 PRJNA1025141 Danio rerio Raw sequence reads PRJNA1025141 Other Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.     Treatment CX2 for transcriptome 2 CX2   strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.66 E|treatment:Treatment Group|BioSampleModel:Model organism or animal                 ALST2 for transcriptome 2 CX2 for transcriptome 2 CX2 for transcriptome 2 CX2 for transcriptome 2     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Ten   SRP465070     Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz fastq fastq 6598066464.0 22061446.0 Unknown AY803 03T0005 good 1.fq.gz 0:149.54 1:149.54 A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217 149 149     1747291499 1543289262 1549193118 1758088368 204217 SRX22027739 SRS19100854 SRA1727563 Soochow University|School of biology & basic medical sciences Soochow University 2 0.88949 0.92148 0.08893 0.0947 0.65596 0.65228 0.46045 0.47087 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2023-10-11 Larval Larval Whole Organism All anatomical structures
28492 28492 SRR26319603 SRX22027738 SRS19100853 SRP465070 PRJNA1025141 Danio rerio Raw sequence reads PRJNA1025141 Other Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.     Treatment CX1 for transcriptome 1 CX1   strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.65 E|treatment:Treatment Group|BioSampleModel:Model organism or animal                 ALST1 for transcriptome 1 CX1 for transcriptome 1 CX1 for transcriptome 1 CX1 for transcriptome 1     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Ten   SRP465070     Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz fastq fastq 6478923586.0 21662443.0 Unknown AY803 03T0004 good 1.fq.gz 0:149.54 1:149.54 A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990 149 149     1712718473 1518937459 1523570227 1723510437 186990 SRX22027738 SRS19100853 SRA1727563 Soochow University|School of biology & basic medical sciences Soochow University 2 0.89423 0.9176 0.08944 0.09254 0.6575 0.65458 0.4693 0.46842 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2023-10-11 Larval Larval Whole Organism All anatomical structures
28493 28493 SRR26319604 SRX22027737 SRS19100856 SRP465070 PRJNA1025141 Danio rerio Raw sequence reads PRJNA1025141 Other Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.     Control con3 for transcriptome 3 con3   strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.64 E|treatment:Control Group|BioSampleModel:Model organism or animal                 con3 for transcriptome 3 con3 for transcriptome 3 con3 for transcriptome 3 con3 for transcriptome 3     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Ten   SRP465070     Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz fastq fastq 6341537566.0 21218597.0 Unknown AY803 03T0003 good 1.fq.gz 0:149.43 1:149.43 A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250 149 149     1679811754 1483631833 1489430825 1688482904 180250 SRX22027737 SRS19100856 SRA1727563 Soochow University|School of biology & basic medical sciences Soochow University 2 0.88245 0.91856 0.09069 0.09654 0.66253 0.65817 0.46245 0.46336 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2023-10-11 Larval Larval Whole Organism All anatomical structures
28494 28494 SRR26319605 SRX22027736 SRS19100855 SRP465070 PRJNA1025141 Danio rerio Raw sequence reads PRJNA1025141 Other Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.     Control con2 for transcriptome 2 con2   strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.63 E|treatment:Control Group|BioSampleModel:Model organism or animal                 con2 for transcriptome 2 con2 for transcriptome 2 con2 for transcriptome 2 con2 for transcriptome 2     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Ten   SRP465070     Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz fastq fastq 5709771178.0 19100144.0 Unknown AY803 03T0002 good 1.fq.gz 0:149.47 1:149.47 A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283 149 149     1505730979 1342843084 1346105868 1514941964 149283 SRX22027736 SRS19100855 SRA1727563 Soochow University|School of biology & basic medical sciences Soochow University 2 0.8924 0.91903 0.09155 0.09604 0.65902 0.65593 0.4634 0.46028 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2023-10-11 Larval Larval Whole Organism All anatomical structures
28495 28495 SRR26319606 SRX22027735 SRS19100852 SRP465070 PRJNA1025141 Danio rerio Raw sequence reads PRJNA1025141 Other Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.     Control con1 for transcriptome 1 con1   strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.62 E|treatment:Control Group|BioSampleModel:Model organism or animal                 con1 for transcriptome 1 con1 for transcriptome 1 con1 for transcriptome 1 con1 for transcriptome 1     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Ten   SRP465070     Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz fastq fastq 6544586118.0 21872265.0 Unknown AY803 03T0001 good 1.fq.gz 0:149.61 1:149.61 A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334 149 149     1731179229 1528367346 1541103688 1743735521 200334 SRX22027735 SRS19100852 SRA1727563 Soochow University|School of biology & basic medical sciences Soochow University 2 0.87588 0.92739 0.08683 0.09494 0.65711 0.6504 0.46774 0.47072 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2023-10-11 Larval Larval Whole Organism All anatomical structures
28985 28985 SRR26936267 SRX22630108 SRS19628590 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 6 GSM7916507   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing La 6 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916507 GSM7916507: La 6; Danio rerio; ncRNA Seq GSM7916507 r1 GSM7916507 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X32_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 810705967.0 27544418.0 GSM7916507 r1 0:29.43 A:141437993;C:173890211;G:258408531;T:236922660;N:46572 29       141437993 173890211 258408531 236922660 46572 SRX22630108 SRS19628590 SRA1756943 University of East Anglia University of East Anglia 1 0.86832   0.1884   0.84735   0.64657   21   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28986 28986 SRR26936231 SRX22630107 SRS19628589 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 5 GSM7916506   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing La 5 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916506 GSM7916506: La 5; Danio rerio; ncRNA Seq GSM7916506 r1 GSM7916506 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X31_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 1237906972.0 45149037.0 GSM7916506 r1 0:27.42 A:273044213;C:252818121;G:368519115;T:343444331;N:81192 27       273044213 252818121 368519115 343444331 81192 SRX22630107 SRS19628589 SRA1756943 University of East Anglia University of East Anglia 1 0.86015   0.25463   0.83798   0.67166   25   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28987 28987 SRR26936232 SRX22630106 SRS19628588 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 2 GSM7916505   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 2 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916505 GSM7916505: Hb 2; Danio rerio; ncRNA Seq GSM7916505 r1 GSM7916505 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X30_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 214730387.0 7217086.0 GSM7916505 r1 0:29.75 A:42819722;C:48080032;G:67677978;T:56140049;N:12606 29       42819722 48080032 67677978 56140049 12606 SRX22630106 SRS19628588 SRA1756943 University of East Anglia University of East Anglia 1 0.85212   0.1617   0.86856   0.69163   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28988 28988 SRR26936233 SRX22630105 SRS19628587 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 1 GSM7916504   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 1 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916504 GSM7916504: Hb 1; Danio rerio; ncRNA Seq GSM7916504 r1 GSM7916504 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X29_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 595989272.0 21399963.0 GSM7916504 r1 0:27.85 A:128259525;C:125823294;G:181746588;T:160121380;N:38485 27       128259525 125823294 181746588 160121380 38485 SRX22630105 SRS19628587 SRA1756943 University of East Anglia University of East Anglia 1 0.85218   0.22941   0.83595   0.6151   30   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28989 28989 SRR26936234 SRX22630104 SRS19628586 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 6 GSM7916503   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 6 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916503 GSM7916503: Lb 6; Danio rerio; ncRNA Seq GSM7916503 r1 GSM7916503 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X28_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 969307398.0 35511411.0 GSM7916503 r1 0:27.30 A:205174189;C:203840471;G:285952255;T:274278193;N:62290 27       205174189 203840471 285952255 274278193 62290 SRX22630104 SRS19628586 SRA1756943 University of East Anglia University of East Anglia 1 0.85414   0.22608   0.8505   0.62202   33   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28990 28990 SRR26936235 SRX22630103 SRS19628585 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 6 GSM7916502   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 6 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916502 GSM7916502: Ha 6; Danio rerio; ncRNA Seq GSM7916502 r1 GSM7916502 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X27_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 1326612630.0 47094729.0 GSM7916502 r1 0:28.17 A:303455697;C:273680466;G:382978796;T:366416311;N:81360 28       303455697 273680466 382978796 366416311 81360 SRX22630103 SRS19628585 SRA1756943 University of East Anglia University of East Anglia 1 0.84786   0.24696   0.82946   0.68975   37   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28991 28991 SRR26936236 SRX22630102 SRS19628584 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 5 GSM7916501   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 5 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916501 GSM7916501: Ha 5; Danio rerio; ncRNA Seq GSM7916501 r1 GSM7916501 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X26_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 471823428.0 16704799.0 GSM7916501 r1 0:28.24 A:103178860;C:100561292;G:155557190;T:112495106;N:30980 28       103178860 100561292 155557190 112495106 30980 SRX22630102 SRS19628584 SRA1756943 University of East Anglia University of East Anglia 1 0.61628   0.14433   0.91275   0.6543   28   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28992 28992 SRR26936237 SRX22630101 SRS19628583 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 4 GSM7916500   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing La 4 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916500 GSM7916500: La 4; Danio rerio; ncRNA Seq GSM7916500 r1 GSM7916500 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X25_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz fastq 713371286.0 25212566.0 GSM7916500 r1 0:28.29 A:155201946;C:151864186;G:207971547;T:198288220;N:45387 28       155201946 151864186 207971547 198288220 45387 SRX22630101 SRS19628583 SRA1756943 University of East Anglia University of East Anglia 1 0.8507   0.2078   0.83031   0.62739   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28993 28993 SRR26936238 SRX22630100 SRS19628582 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 5 GSM7916499   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 5 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916499 GSM7916499: Hb 5; Danio rerio; ncRNA Seq GSM7916499 r1 GSM7916499 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X24_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 1043060550.0 35761504.0 GSM7916499 r1 0:29.17 A:217942105;C:216398395;G:316456102;T:292217159;N:46789 29       217942105 216398395 316456102 292217159 46789 SRX22630100 SRS19628582 SRA1756943 University of East Anglia University of East Anglia 1 0.82114   0.20881   0.85622   0.68486   19   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28994 28994 SRR26936239 SRX22630099 SRS19628581 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 4 GSM7916498   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 4 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916498 GSM7916498: Hb 4; Danio rerio; ncRNA Seq GSM7916498 r1 GSM7916498 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X23_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 1357956641.0 47869361.0 GSM7916498 r1 0:28.37 A:293740473;C:276333777;G:404639503;T:383181225;N:61663 28       293740473 276333777 404639503 383181225 61663 SRX22630099 SRS19628581 SRA1756943 University of East Anglia University of East Anglia 1 0.79885   0.22306   0.8425   0.6656   26   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28995 28995 SRR26936240 SRX22630098 SRS19628580 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 5 GSM7916497   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 5 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916497 GSM7916497: Lb 5; Danio rerio; ncRNA Seq GSM7916497 r1 GSM7916497 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X22_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 669771811.0 23848259.0 GSM7916497 r1 0:28.08 A:132916986;C:135594797;G:198730347;T:202498953;N:30728 28       132916986 135594797 198730347 202498953 30728 SRX22630098 SRS19628580 SRA1756943 University of East Anglia University of East Anglia 1 0.80999   0.24188   0.84658   0.68339   20   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28996 28996 SRR26936241 SRX22630097 SRS19628579 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 4 GSM7916496   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 4 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916496 GSM7916496: Ha 4; Danio rerio; ncRNA Seq GSM7916496 r1 GSM7916496 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X21_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 853803123.0 28538725.0 GSM7916496 r1 0:29.92 A:158220512;C:186146914;G:264519321;T:244878221;N:38155 29       158220512 186146914 264519321 244878221 38155 SRX22630097 SRS19628579 SRA1756943 University of East Anglia University of East Anglia 1 0.828   0.18458   0.85851   0.6483   32   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28997 28997 SRR26936242 SRX22630096 SRS19628578 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 3 GSM7916495   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 3 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916495 GSM7916495: Ha 3; Danio rerio; ncRNA Seq GSM7916495 r1 GSM7916495 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X20_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 629106097.0 21383957.0 GSM7916495 r1 0:29.42 A:117216944;C:131994022;G:192623524;T:187243523;N:28084 29       117216944 131994022 192623524 187243523 28084 SRX22630096 SRS19628578 SRA1756943 University of East Anglia University of East Anglia 1 0.8166   0.20457   0.84112   0.65357   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28998 28998 SRR26936243 SRX22630095 SRS19628577 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 1 GSM7916494   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing La 1 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916494 GSM7916494: La 1; Danio rerio; ncRNA Seq GSM7916494 r1 GSM7916494 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X19_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 21178378.0 739280.0 GSM7916494 r1 0:28.65 A:4323144;C:4478932;G:6303136;T:6072190;N:976 28       4323144 4478932 6303136 6072190 976 SRX22630095 SRS19628577 SRA1756943 University of East Anglia University of East Anglia 1 0.85277   0.21158   0.87434   0.62601   26   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
28999 28999 SRR26936244 SRX22630094 SRS19628576 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 4 GSM7916493   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 4 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916493 GSM7916493: Lb 4; Danio rerio; ncRNA Seq GSM7916493 r1 GSM7916493 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X18_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 959247745.0 33043430.0 GSM7916493 r1 0:29.03 A:225208425;C:212535680;G:284062577;T:237397072;N:43991 29       225208425 212535680 284062577 237397072 43991 SRX22630094 SRS19628576 SRA1756943 University of East Anglia University of East Anglia 1 0.82232   0.22592   0.87073   0.6135   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29000 29000 SRR26936245 SRX22630093 SRS19628575 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 3 GSM7916492   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing Lb 3 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916492 GSM7916492: Lb 3; Danio rerio; ncRNA Seq GSM7916492 r1 GSM7916492 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X17_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz fastq 900287704.0 31947371.0 GSM7916492 r1 0:28.18 A:224093089;C:188919051;G:262824615;T:224407166;N:43783 28       224093089 188919051 262824615 224407166 43783 SRX22630093 SRS19628575 SRA1756943 University of East Anglia University of East Anglia 1 0.67003   0.17024   0.87095   0.6869   19   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29001 29001 SRR26936246 SRX22630092 SRS19628574 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 3 GSM7916491   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Hb 3 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916491 GSM7916491: Hb 3; Danio rerio; ncRNA Seq GSM7916491 r1 GSM7916491 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X16_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 80986783.0 3427704.0 GSM7916491 r1 0:23.63 A:18164838;C:19014879;G:24153410;T:19641723;N:11933 23       18164838 19014879 24153410 19641723 11933 SRX22630092 SRS19628574 SRA1756943 University of East Anglia University of East Anglia 1 0.83312   0.24402   0.88749   0.63345   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29002 29002 SRR26936247 SRX22630091 SRS19628573 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 3 GSM7916490   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing La 3 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916490 GSM7916490: La 3; Danio rerio; ncRNA Seq GSM7916490 r1 GSM7916490 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X15_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 148933985.0 6314805.0 GSM7916490 r1 0:23.58 A:39058546;C:30363738;G:44242466;T:35240575;N:28660 23       39058546 30363738 44242466 35240575 28660 SRX22630091 SRS19628573 SRA1756943 University of East Anglia University of East Anglia 1 0.41302   0.13369   0.89802   0.57553   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29003 29003 SRR26936248 SRX22630090 SRS19628572 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 2 GSM7916489   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing La 2 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916489 GSM7916489: La 2; Danio rerio; ncRNA Seq GSM7916489 r1 GSM7916489 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X14_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 538382421.0 23079847.0 GSM7916489 r1 0:23.33 A:119659971;C:112896468;G:162693210;T:143063074;N:69698 23       119659971 112896468 162693210 143063074 69698 SRX22630090 SRS19628572 SRA1756943 University of East Anglia University of East Anglia 1 0.81532   0.23945   0.8758   0.62425   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29004 29004 SRR26936249 SRX22630089 SRS19628571 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 1 GSM7916488   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 1 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916488 GSM7916488: Ha 1; Danio rerio; ncRNA Seq GSM7916488 r1 GSM7916488 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X13_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 761541737.0 32310434.0 GSM7916488 r1 0:23.57 A:182485471;C:173949932;G:214306916;T:190683160;N:116258 23       182485471 173949932 214306916 190683160 116258 SRX22630089 SRS19628571 SRA1756943 University of East Anglia University of East Anglia 1 0.82936   0.23022   0.85098   0.59571   19   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29005 29005 SRR26936250 SRX22630088 SRS19628570 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 2 GSM7916487   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 2 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916487 GSM7916487: Lb 2; Danio rerio; ncRNA Seq GSM7916487 r1 GSM7916487 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X12_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 559417322.0 23757934.0 GSM7916487 r1 0:23.55 A:126286771;C:106333997;G:170445137;T:156287131;N:64286 23       126286771 106333997 170445137 156287131 64286 SRX22630088 SRS19628570 SRA1756943 University of East Anglia University of East Anglia 1 0.85098   0.26224   0.8608   0.59344   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29006 29006 SRR26936251 SRX22630087 SRS19628569 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 1 GSM7916486   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Lb 1 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916486 GSM7916486: Lb 1; Danio rerio; ncRNA Seq GSM7916486 r1 GSM7916486 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X11_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 498695572.0 21269833.0 GSM7916486 r1 0:23.45 A:122716879;C:84997892;G:144626268;T:146292630;N:61903 23       122716879 84997892 144626268 146292630 61903 SRX22630087 SRS19628569 SRA1756943 University of East Anglia University of East Anglia 1 0.84251   0.1958   0.8591   0.61008   24   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29007 29007 SRR26936252 SRX22630086 SRS19628568 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 10 GSM7916485   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing Hb 10 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916485 GSM7916485: Hb 10; Danio rerio; ncRNA Seq GSM7916485 r1 GSM7916485 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X10_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 686865211.0 29320389.0 GSM7916485 r1 0:23.43 A:156131568;C:132162427;G:201526230;T:196961742;N:83244 23       156131568 132162427 201526230 196961742 83244 SRX22630086 SRS19628568 SRA1756943 University of East Anglia University of East Anglia 1 0.85707   0.27856   0.85648   0.59717   28   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29008 29008 SRR26936253 SRX22630085 SRS19628567 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 9 GSM7916484   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing La 9 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916484 GSM7916484: La 9; Danio rerio; ncRNA Seq GSM7916484 r1 GSM7916484 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X9_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz fastq 561289514.0 23860643.0 GSM7916484 r1 0:23.52 A:140848879;C:98838555;G:161520871;T:160013845;N:67364 23       140848879 98838555 161520871 160013845 67364 SRX22630085 SRS19628567 SRA1756943 University of East Anglia University of East Anglia 1 0.85507   0.17768   0.86969   0.64792   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29009 29009 SRR26936254 SRX22630084 SRS19628566 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 8 GSM7916483   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing La 8 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916483 GSM7916483: La 8; Danio rerio; ncRNA Seq GSM7916483 r1 GSM7916483 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X8_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 458491681.0 16224249.0 GSM7916483 r1 0:28.26 A:99631677;C:90884289;G:139467457;T:128470855;N:37403 28       99631677 90884289 139467457 128470855 37403 SRX22630084 SRS19628566 SRA1756943 University of East Anglia University of East Anglia 1 0.81704   0.21909   0.84762   0.6293   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29010 29010 SRR26936255 SRX22630083 SRS19628565 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 9 GSM7916482   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing Ha 9 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916482 GSM7916482: Ha 9; Danio rerio; ncRNA Seq GSM7916482 r1 GSM7916482 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X7_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 574511047.0 20295283.0 GSM7916482 r1 0:28.31 A:134481373;C:122719422;G:169313406;T:147944946;N:51900 28       134481373 122719422 169313406 147944946 51900 SRX22630083 SRS19628565 SRA1756943 University of East Anglia University of East Anglia 1 0.81932   0.19984   0.85987   0.58268   23   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29011 29011 SRR26936256 SRX22630082 SRS19628564 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 8 GSM7916481   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 8 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916481 GSM7916481: Lb 8; Danio rerio; ncRNA Seq GSM7916481 r1 GSM7916481 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X6_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 1086899780.0 37486748.0 GSM7916481 r1 0:28.99 A:219996636;C:232899819;G:335644980;T:298269921;N:88424 28       219996636 232899819 335644980 298269921 88424 SRX22630082 SRS19628564 SRA1756943 University of East Anglia University of East Anglia 1 0.86943   0.2105   0.84461   0.67703   44   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29012 29012 SRR26936257 SRX22630081 SRS19628563 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 9 GSM7916480   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 9 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916480 GSM7916480: Hb 9; Danio rerio; ncRNA Seq GSM7916480 r1 GSM7916480 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X5_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 1144093618.0 39048750.0 GSM7916480 r1 0:29.30 A:223769668;C:238953593;G:358148504;T:323130325;N:91528 29       223769668 238953593 358148504 323130325 91528 SRX22630081 SRS19628563 SRA1756943 University of East Anglia University of East Anglia 1 0.87445   0.1906   0.87237   0.70919   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29013 29013 SRR26936258 SRX22630080 SRS19628562 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 7 GSM7916515   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 7 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916515 GSM7916515: Hb 7; Danio rerio; ncRNA Seq GSM7916515 r1 GSM7916515 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X40_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 263782568.0 9802454.0 GSM7916515 r1 0:26.91 A:59378855;C:53589034;G:83219251;T:67574216;N:21212 26       59378855 53589034 83219251 67574216 21212 SRX22630080 SRS19628562 SRA1756943 University of East Anglia University of East Anglia 1 0.80146   0.31524   0.81008   0.47305   30   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29014 29014 SRR26936260 SRX22630079 SRS19628561 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 8 GSM7916514   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 8 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916514 GSM7916514: Ha 8; Danio rerio; ncRNA Seq GSM7916514 r1 GSM7916514 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X39_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 252119227.0 9309447.0 GSM7916514 r1 0:27.08 A:53293803;C:51577689;G:79148986;T:68078043;N:20706 27       53293803 51577689 79148986 68078043 20706 SRX22630079 SRS19628561 SRA1756943 University of East Anglia University of East Anglia 1 0.75593   0.29042   0.83412   0.59657   21   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29015 29015 SRR26936261 SRX22630078 SRS19628560 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 6 GSM7916513   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 6 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916513 GSM7916513: Hb 6; Danio rerio; ncRNA Seq GSM7916513 r1 GSM7916513 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X38_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 516408240.0 19719085.0 GSM7916513 r1 0:26.19 A:112791146;C:102652986;G:160354602;T:140566375;N:43131 26       112791146 102652986 160354602 140566375 43131 SRX22630078 SRS19628560 SRA1756943 University of East Anglia University of East Anglia 1 0.80401   0.31982   0.83765   0.57755   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29016 29016 SRR26936262 SRX22630077 SRS19628559 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 7 GSM7916512   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 7 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916512 GSM7916512: Ha 7; Danio rerio; ncRNA Seq GSM7916512 r1 GSM7916512 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X37_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 554171558.0 20779285.0 GSM7916512 r1 0:26.67 A:125256371;C:111354628;G:172197000;T:145317427;N:46132 26       125256371 111354628 172197000 145317427 46132 SRX22630077 SRS19628559 SRA1756943 University of East Anglia University of East Anglia 1 0.81035   0.28326   0.82933   0.62525   35   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29017 29017 SRR26936263 SRX22630076 SRS19628558 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 10 GSM7916511   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 10 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916511 GSM7916511: Lb 10; Danio rerio; ncRNA Seq GSM7916511 r1 GSM7916511 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X36_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 983846643.0 32513493.0 GSM7916511 r1 0:30.26 A:181840038;C:211101778;G:320659770;T:270174775;N:70282 30       181840038 211101778 320659770 270174775 70282 SRX22630076 SRS19628558 SRA1756943 University of East Anglia University of East Anglia 1 0.88133   0.15829   0.86324   0.67761   37   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29018 29018 SRR26936264 SRX22630075 SRS19628557 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 9 GSM7916510   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing Lb 9 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low2 GSM7916510 GSM7916510: Lb 9; Danio rerio; ncRNA Seq GSM7916510 r1 GSM7916510 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X35_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 1077131964.0 37869598.0 GSM7916510 r1 0:28.44 A:210508796;C:220304812;G:327237157;T:319001223;N:79976 28       210508796 220304812 327237157 319001223 79976 SRX22630075 SRS19628557 SRA1756943 University of East Anglia University of East Anglia 1 0.84871   0.22867   0.83968   0.66027   35   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29019 29019 SRR26936265 SRX22630074 SRS19628556 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Lb 7 GSM7916509   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing Lb 7 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916509 GSM7916509: Lb 7; Danio rerio; ncRNA Seq GSM7916509 r1 GSM7916509 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X34_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 1203153474.0 42565421.0 GSM7916509 r1 0:28.27 A:269760359;C:263088083;G:348288367;T:321910116;N:106549 28       269760359 263088083 348288367 321910116 106549 SRX22630074 SRS19628556 SRA1756943 University of East Anglia University of East Anglia 1 0.82319   0.21661   0.82432   0.65954   33   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29020 29020 SRR26936266 SRX22630073 SRS19628555 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 7 GSM7916508   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing La 7 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916508 GSM7916508: La 7; Danio rerio; ncRNA Seq GSM7916508 r1 GSM7916508 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X33_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz fastq 1137464666.0 42434385.0 GSM7916508 r1 0:26.81 A:240256314;C:218420241;G:336730784;T:341968066;N:89261 26       240256314 218420241 336730784 341968066 89261 SRX22630073 SRS19628555 SRA1756943 University of East Anglia University of East Anglia 1 0.84647   0.26357   0.85313   0.67665   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29021 29021 SRR26936259 SRX22630072 SRS19628554 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Hb 8 GSM7916479   tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing Hb 8 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High2 GSM7916479 GSM7916479: Hb 8; Danio rerio; ncRNA Seq GSM7916479 r1 GSM7916479 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X4_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 1014850001.0 36540733.0 GSM7916479 r1 0:27.77 A:205870762;C:199482442;G:294628769;T:314783528;N:84500 27       205870762 199482442 294628769 314783528 84500 SRX22630072 SRS19628554 SRA1756943 University of East Anglia University of East Anglia 1 0.84303   0.28884   0.81692   0.66059   26   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29022 29022 SRR26936268 SRX22630071 SRS19628553 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   La 10 GSM7916478   tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing La 10 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:Low1 GSM7916478 GSM7916478: La 10; Danio rerio; ncRNA Seq GSM7916478 r1 GSM7916478 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X3_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 916186556.0 32659639.0 GSM7916478 r1 0:28.05 A:216314501;C:191651870;G:267047552;T:241092719;N:79914 28       216314501 191651870 267047552 241092719 79914 SRX22630071 SRS19628553 SRA1756943 University of East Anglia University of East Anglia 1 0.84312   0.23836   0.83132   0.57754   33   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29023 29023 SRR26936269 SRX22630070 SRS19628552 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 10 GSM7916477   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 10 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916477 GSM7916477: Ha 10; Danio rerio; ncRNA Seq GSM7916477 r1 GSM7916477 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X2_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 858990742.0 30463457.0 GSM7916477 r1 0:28.20 A:182799146;C:179417249;G:265490509;T:231201694;N:82144 28       182799146 179417249 265490509 231201694 82144 SRX22630070 SRS19628552 SRA1756943 University of East Anglia University of East Anglia 1 0.67221   0.19137   0.87986   0.67831   33   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29024 29024 SRR26936270 SRX22630069 SRS19628551 SRP473892 PRJNA1044439 Social stress in fathers affects sperm small RNA and offspring transcriptome profiles GSE248535 Transcriptome Analysis Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments with sperm samples collected RNA extracted and sent for small RNA sequencing.   pubmed:40121340   Ha 2 GSM7916476   tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing Ha 2 Reads were trimmed aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39 so this sample was omitted from analyses. sperm   Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   cell line:sperm|genotype:WT|treatment:High1 GSM7916476 GSM7916476: Ha 2; Danio rerio; ncRNA Seq GSM7916476 r1 GSM7916476 1 Total RNA extraction New England BioLabs kit NEBNext®Multiplex Small RNA Library Prep Set for Illumina® Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP473892     12235X1_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz fastq 262855265.0 9317037.0 GSM7916476 r1 0:28.21 A:59555006;C:56655912;G:79385169;T:67236972;N:22206 28       59555006 56655912 79385169 67236972 22206 SRX22630069 SRS19628551 SRA1756943 University of East Anglia University of East Anglia 1 0.85088   0.21543   0.84102   0.63415   28   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   United Kingdom 2023-11-23 Undetermined Embryo Cell Line Cell Line
29739 29739 SRR27467672 SRX23139234 SRS20090275 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf mock rep2 EV04009 EV04009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04009.R1.fastq.gz fastq 609590940.0 4354221.0 EV04009.R1.fastq.gz 0:140 A:155062144;C:147628702;G:168099121;T:138772205;N:28768 140       155062144 147628702 168099121 138772205 28768 SRX23139234 SRS20090275 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29740 29740 SRR27467673 SRX23139233 SRS20090278 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf BS rep2 EV04008 EV04008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04008.R1.fastq.gz fastq 675505180.0 4825037.0 EV04008.R1.fastq.gz 0:140 A:178823976;C:121648962;G:198428643;T:176572292;N:31307 140       178823976 121648962 198428643 176572292 31307 SRX23139233 SRS20090278 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29741 29741 SRR27467674 SRX23139232 SRS20090272 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf DM rep2 EV04007 EV04007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04007.R1.fastq.gz fastq 702064440.0 5014746.0 EV04007.R1.fastq.gz 0:140 A:176719694;C:166467163;G:207893965;T:150951950;N:31668 140       176719694 166467163 207893965 150951950 31668 SRX23139232 SRS20090272 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29742 29742 SRR27467675 SRX23139231 SRS20090271 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf mock rep2 EV04006 EV04006 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04006.R1.fastq.gz fastq 664790700.0 4748505.0 EV04006.R1.fastq.gz 0:140 A:172014219;C:146545691;G:200358431;T:145840649;N:31710 140       172014219 146545691 200358431 145840649 31710 SRX23139231 SRS20090271 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99993   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29743 29743 SRR27467676 SRX23139230 SRS20090273 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep2 EV04004 EV04004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04004.R1.fastq.gz fastq 895671560.0 6397654.0 EV04004.R1.fastq.gz 0:140 A:206443066;C:147067097;G:365386937;T:176734600;N:39860 140       206443066 147067097 365386937 176734600 39860 SRX23139230 SRS20090273 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29744 29744 SRR27467677 SRX23139229 SRS20090274 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep2 EV04003 EV04003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04003.R1.fastq.gz fastq 664112120.0 4743658.0 EV04003.R1.fastq.gz 0:140 A:163711695;C:142612940;G:211194350;T:146562626;N:30509 140       163711695 142612940 211194350 146562626 30509 SRX23139229 SRS20090274 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29745 29745 SRR27467678 SRX23139228 SRS20090268 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: eggs mock rep2 EV04001 EV04001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04001.R1.fastq.gz fastq 970037880.0 6928842.0 EV04001.R1.fastq.gz 0:140 A:258735538;C:237798398;G:268588390;T:204871983;N:43571 140       258735538 237798398 268588390 204871983 43571 SRX23139228 SRS20090268 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Undetermined Embryo Undetermined Embryo Imprecise
29746 29746 SRR27467679 SRX23139227 SRS20090270 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep2 EV02003 EV02003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02003.R1.fastq.gz EV02003.R2.fastq.gz fastq fastq 1031891720.0 3416860.0 EV02003.R1.fastq.gz 0:151 1:151 A:264464363;C:153440613;G:408557241;T:205367487;N:62016 151 151     264464363 153440613 408557241 205367487 62016 SRX23139227 SRS20090270 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 0.0 0.00019 0.0 0.00015 1.0 0.99993   1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29747 29747 SRR27467680 SRX23139226 SRS20090267 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf BS rep2 EV03009 EV03009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV03009.R1.fastq.gz fastq 168931280.0 2222780.0 EV03009.R1.fastq.gz 0:76 A:49803604;C:36479774;G:37758990;T:44874154;N:14758 76       49803604 36479774 37758990 44874154 14758 SRX23139226 SRS20090267 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00034   0.0002   0.99965   0.5   76   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Pharyngula Embryo Whole Organism All anatomical structures
29748 29748 SRR27467681 SRX23139225 SRS20090266 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf DM rep2 EV03008 EV03008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV03008.R1.fastq.gz fastq 200878792.0 2643142.0 EV03008.R1.fastq.gz 0:76 A:46955288;C:54746275;G:55887832;T:43270561;N:18836 76       46955288 54746275 55887832 43270561 18836 SRX23139225 SRS20090266 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.29408   0.00737   0.91823   0.54549   76   B   usable mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Pharyngula Embryo Whole Organism All anatomical structures
29749 29749 SRR27467682 SRX23139224 SRS20090269 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf mock rep2 EV03007 EV03007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV03007.R1.fastq.gz fastq 175642840.0 2311090.0 EV03007.R1.fastq.gz 0:76 A:44745275;C:48908904;G:44862157;T:37111895;N:14609 76       44745275 48908904 44862157 37111895 14609 SRX23139224 SRS20090269 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.06887   0.00273   0.96623   0.48721   76   B   usable mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Pharyngula Embryo Whole Organism All anatomical structures
29750 29750 SRR27467683 SRX23139223 SRS20090265 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf BS rep2 EV04014 EV04014 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04014.R1.fastq.gz fastq 774901260.0 5535009.0 EV04014.R1.fastq.gz 0:140 A:193865579;C:138861953;G:251102013;T:191036071;N:35644 140       193865579 138861953 251102013 191036071 35644 SRX23139223 SRS20090265 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Gastrula Embryo Whole Organism All anatomical structures
29751 29751 SRR27467684 SRX23139222 SRS20090264 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf DM rep2 EV04013 EV04013 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04013.R1.fastq.gz fastq 666372840.0 4759806.0 EV04013.R1.fastq.gz 0:140 A:172923134;C:142243998;G:211584978;T:139591020;N:29710 140       172923134 142243998 211584978 139591020 29710 SRX23139222 SRS20090264 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99991   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Gastrula Embryo Whole Organism All anatomical structures
29752 29752 SRR27467685 SRX23139221 SRS20090262 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf mock rep2 EV04012 EV04012 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04012.R1.fastq.gz fastq 628769540.0 4491211.0 EV04012.R1.fastq.gz 0:140 A:160925901;C:143204697;G:183224867;T:141385307;N:28768 140       160925901 143204697 183224867 141385307 28768 SRX23139221 SRS20090262 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Gastrula Embryo Whole Organism All anatomical structures
29753 29753 SRR27467686 SRX23139220 SRS20090263 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf BS rep2 EV04011 EV04011 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04011.R1.fastq.gz fastq 720913200.0 5149380.0 EV04011.R1.fastq.gz 0:140 A:185414155;C:126110104;G:238649631;T:170706590;N:32720 140       185414155 126110104 238649631 170706590 32720 SRX23139220 SRS20090263 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29754 29754 SRR27467687 SRX23139219 SRS20090259 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf DM rep2 EV04010 EV04010 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04010.R1.fastq.gz fastq 443650200.0 3168930.0 EV04010.R1.fastq.gz 0:140 A:114663509;C:102512276;G:135709753;T:90744641;N:20021 140       114663509 102512276 135709753 90744641 20021 SRX23139219 SRS20090259 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29755 29755 SRR27467688 SRX23139218 SRS20090261 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep2 EV02002 EV02002 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02002.R1.fastq.gz EV02002.R2.fastq.gz fastq fastq 861320308.0 2852054.0 EV02002.R1.fastq.gz 0:151 1:151 A:205625519;C:162178974;G:334206312;T:159256900;N:52603 151 151     205625519 162178974 334206312 159256900 52603 SRX23139218 SRS20090261 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00049 0.0 0.00027 1.0 0.99947   0.44444 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29756 29756 SRR27467689 SRX23139217 SRS20090260 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep2 EV02001 EV02001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02001.R1.fastq.gz EV02001.R2.fastq.gz fastq fastq 520371066.0 1723083.0 EV02001.R1.fastq.gz 0:151 1:151 A:116107273;C:90896560;G:218652568;T:94682244;N:32421 151 151     116107273 90896560 218652568 94682244 32421 SRX23139217 SRS20090260 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00086 0.0 0.00078 0.99995 0.99981 0.0 0.61538 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29757 29757 SRR27437477 SRX23109820 SRS20064574 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf mock rep3 EV07007 EV07007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07007.R1.fastq.gz fastq 479994620.0 3428533.0 EV07007.R1.fastq.gz 0:140 A:124628886;C:116843590;G:123136721;T:115372734;N:12689 140       124628886 116843590 123136721 115372734 12689 SRX23109820 SRS20064574 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 6e-05   1e-05   0.99989   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29758 29758 SRR27437478 SRX23109819 SRS20064573 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep3 EV07006 EV07006 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07006.R1.fastq.gz fastq 2584527680.0 18460912.0 EV07006.R1.fastq.gz 0:140 A:685107500;C:367766834;G:717359848;T:814224206;N:69292 140       685107500 367766834 717359848 814224206 69292 SRX23109819 SRS20064573 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   1e-05   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29759 29759 SRR27437479 SRX23109818 SRS20064571 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep3 EV07005 EV07005 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07005.R1.fastq.gz fastq 713829480.0 5098782.0 EV07005.R1.fastq.gz 0:140 A:183575304;C:168886779;G:213156258;T:148191838;N:19301 140       183575304 168886779 213156258 148191838 19301 SRX23109818 SRS20064571 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 5e-05   0.0   0.99989   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29760 29760 SRR27437480 SRX23109817 SRS20064572 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep3 EV07004 EV07004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07004.R1.fastq.gz fastq 517336680.0 3695262.0 EV07004.R1.fastq.gz 0:140 A:136783049;C:131207858;G:139873280;T:109458276;N:14217 140       136783049 131207858 139873280 109458276 14217 SRX23109817 SRS20064572 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 7e-05   0.0   0.99981   0.7   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29761 29761 SRR27437481 SRX23109816 SRS20064569 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: eggs BS rep3 EV07003 EV07003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07003.R1.fastq.gz fastq 688960160.0 4921144.0 EV07003.R1.fastq.gz 0:140 A:187831021;C:119362814;G:195214528;T:186533242;N:18555 140       187831021 119362814 195214528 186533242 18555 SRX23109816 SRS20064569 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Undetermined Embryo Undetermined Embryo Imprecise
29762 29762 SRR27437482 SRX23109815 SRS20064568 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: eggs DM rep3 EV07002 EV07002 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07002.R1.fastq.gz fastq 520725380.0 3719467.0 EV07002.R1.fastq.gz 0:140 A:138972126;C:125739732;G:142785467;T:113214166;N:13889 140       138972126 125739732 142785467 113214166 13889 SRX23109815 SRS20064568 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00014   1e-05   0.99969   0.5   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Undetermined Embryo Undetermined Embryo Imprecise
29763 29763 SRR27437483 SRX23109814 SRS20064570 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: eggs mock rep3 EV07001 EV07001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07001.R1.fastq.gz fastq 684538960.0 4889564.0 EV07001.R1.fastq.gz 0:140 A:178906891;C:169237174;G:192342342;T:144034095;N:18458 140       178906891 169237174 192342342 144034095 18458 SRX23109814 SRS20064570 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0001   1e-05   0.99977   0.76923   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Undetermined Embryo Undetermined Embryo Imprecise
29764 29764 SRR27437484 SRX23109813 SRS20064567 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf BS rep3 EV07018 EV07018 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07018.R1.fastq.gz fastq 887731180.0 6340937.0 EV07018.R1.fastq.gz 0:140 A:204102176;C:148262233;G:350287017;T:185056779;N:22975 140       204102176 148262233 350287017 185056779 22975 SRX23109813 SRS20064567 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Pharyngula Embryo Whole Organism All anatomical structures
29765 29765 SRR27437485 SRX23109812 SRS20064566 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep3 EV04017 EV04017 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04017.R1.fastq.gz fastq 576584540.0 4118461.0 EV04017.R1.fastq.gz 0:140 A:149516980;C:91163801;G:169046762;T:166831111;N:25886 140       149516980 91163801 169046762 166831111 25886 SRX23109812 SRS20064566 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive 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");;