{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Gastrula\" and technology = \"bulk\"", "rows": [[25273, "SRR25764091", "SRX21486763", "SRS18719063", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "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", null, "WT bud 10 hpf RNA seq rep2", "GSM7734768", null, "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 RNA seq rep2", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "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. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT", "GSM7734768", "GSM7734768: WT bud 10 hpf RNA seq rep2; Danio rerio; RNA Seq", "GSM7734768 r1", "GSM7734768", "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. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_bud_2.fastq.gz", "fastq", 2470912004.0, 31168086.0, "GSM7734768 r1", "0:79.28", "A:656817108;C:568241258;G:504262095;T:741507737;N:83806", 79, null, null, null, 656817108, 568241258, 504262095, 741507737, 83806, "SRX21486763", "SRS18719063", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.91479, null, 0.27298, null, 0.74231, null, 0.57302, null, 79, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [25274, "SRR25764092", "SRX21486762", "SRS18719064", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "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", null, "WT bud 10 hpf RNA seq rep1", "GSM7734767", null, "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 RNA seq rep1", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "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. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT", "GSM7734767", "GSM7734767: WT bud 10 hpf RNA seq rep1; Danio rerio; RNA Seq", "GSM7734767 r1", "GSM7734767", "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. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_bud_1.fastq.gz", "fastq", 2153494756.0, 27140032.0, "GSM7734767 r1", "0:79.35", "A:560793143;C:508962676;G:445126772;T:638539310;N:72855", 79, null, null, null, 560793143, 508962676, 445126772, 638539310, 72855, "SRX21486762", "SRS18719064", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.88728, null, 0.25493, null, 0.74369, null, 0.56589, null, 80, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [30031, "SRR27732027", "SRX23397621", "SRS20258462", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 8 hpf embryo", "zebrafish embryo 8hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 8hpf embryo", "W 6", "W 6", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT8h-3_2.fq.gz WT8h-3_1.fq.gz", "fastq fastq", 6747267300.0, 22490891.0, "WT8h 3 1.fq.gz", "0:150 1:150", "A:1802220913;C:1560718919;G:1610360895;T:1773867706;N:98867", 150, 150, null, null, 1802220913, 1560718919, 1610360895, 1773867706, 98867, "SRX23397621", "SRS20258462", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94669, 0.94524, 0.06343, 0.06321, 0.74517, 0.74535, 0.46737, 0.46861, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30040, "SRR27732036", "SRX23397612", "SRS20258453", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 8 hpf embryo", "zebrafish embryo 8hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 8hpf embryo", "W 5", "W 5", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT8h-2_1.fq.gz WT8h-2_2.fq.gz", "fastq fastq", 6832373100.0, 22774577.0, "WT8h 2 1.fq.gz", "0:150 1:150", "A:1819536066;C:1586031035;G:1634106671;T:1792464818;N:234510", 150, 150, null, null, 1819536066, 1586031035, 1634106671, 1792464818, 234510, "SRX23397612", "SRS20258453", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94411, 0.94402, 0.0643, 0.06343, 0.7472, 0.74775, 0.47176, 0.46993, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30041, "SRR27732037", "SRX23397611", "SRS20258452", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 8 hpf embryo", "zebrafish embryo 8hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 8hpf embryo", "W 4", "W 4", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT8h-1_1.fq.gz WT8h-1_2.fq.gz", "fastq fastq", 5792885100.0, 19309617.0, "WT8h 1 1.fq.gz", "0:150 1:150", "A:1545377384;C:1341340578;G:1388087015;T:1517986965;N:93158", 150, 150, null, null, 1545377384, 1341340578, 1388087015, 1517986965, 93158, "SRX23397611", "SRS20258452", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94512, 0.9415, 0.05988, 0.05963, 0.74345, 0.74582, 0.46534, 0.46722, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30046, "SRR27730709", "SRX23396349", "SRS20257263", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 8 hpf embryo", "zebrafish embryo hamp / 8hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 8hpf embryo", "W 27", "W 27", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp8h-3_1.fq.gz hamp8h-3_2.fq.gz", "fastq fastq", 6295202100.0, 20984007.0, "hamp8h 3 1.fq.gz", "0:150 1:150", "A:1694806329;C:1445372178;G:1488024762;T:1666904080;N:94751", 150, 150, null, null, 1694806329, 1445372178, 1488024762, 1666904080, 94751, "SRX23396349", "SRS20257263", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94405, 0.94297, 0.06722, 0.06702, 0.76627, 0.76828, 0.48464, 0.48699, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30047, "SRR27730710", "SRX23396348", "SRS20257262", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 8 hpf embryo", "zebrafish embryo hamp / 8hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 8hpf embryo", "W 26", "W 26", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp8h-2_1.fq.gz hamp8h-2_2.fq.gz", "fastq fastq", 6148660800.0, 20495536.0, "hamp8h 2 1.fq.gz", "0:150 1:150", "A:1644992837;C:1420391182;G:1458975922;T:1624091150;N:209709", 150, 150, null, null, 1644992837, 1420391182, 1458975922, 1624091150, 209709, "SRX23396348", "SRS20257262", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93828, 0.93748, 0.08438, 0.08432, 0.74681, 0.74732, 0.48765, 0.48809, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30048, "SRR27730711", "SRX23396347", "SRS20257261", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 8 hpf embryo", "zebrafish embryo hamp / 8hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 8hpf embryo", "W 25", "W 25", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp8h-1_1.fq.gz hamp8h-1_2.fq.gz", "fastq fastq", 7443429000.0, 24811430.0, "hamp8h 1 1.fq.gz", "0:150 1:150", "A:1989642168;C:1723187805;G:1770726575;T:1959761293;N:111159", 150, 150, null, null, 1989642168, 1723187805, 1770726575, 1959761293, 111159, "SRX23396347", "SRS20257261", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94417, 0.94323, 0.06281, 0.06203, 0.76479, 0.76706, 0.47849, 0.4799, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30763, "SRR28348929", "SRX23954967", "SRS20755388", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp stage III oocytes germinal vesicle in central position at 4\u20137 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf hpf 2 hpf 4 hpf and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo 6hpf rep3", "GSM8147864", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:6hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo 6hpf rep3", "Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:6hpf|genotype:AB TF and TLF", "GSM8147864", "GSM8147864: Zebrafish Embryo 6hpf rep3; Danio rerio; RNA Seq", "GSM8147864 r1", "GSM8147864", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_6hpf_3.fastq", "fastq", 1995475456.0, 26256256.0, "GSM8147864 r1", "0:76", "A:476287182;C:495924342;G:473333224;T:549838609;N:92099", 76, null, null, null, 476287182, 495924342, 473333224, 549838609, 92099, "SRX23954967", "SRS20755388", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [30764, "SRR28348930", "SRX23954966", "SRS20755387", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp stage III oocytes germinal vesicle in central position at 4\u20137 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf hpf 2 hpf 4 hpf and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo 6hpf rep2", "GSM8147863", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:6hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo 6hpf rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:6hpf|genotype:AB TF and TLF", "GSM8147863", "GSM8147863: Zebrafish Embryo 6hpf rep2; Danio rerio; RNA Seq", "GSM8147863 r1", "GSM8147863", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_6hpf_2.fastq", "fastq", 1879805128.0, 24734278.0, "GSM8147863 r1", "0:76", "A:459381268;C:457619912;G:436198103;T:526517368;N:88477", 76, null, null, null, 459381268, 457619912, 436198103, 526517368, 88477, "SRX23954966", "SRS20755387", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [30765, "SRR28348931", "SRX23954965", "SRS20755386", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp stage III oocytes germinal vesicle in central position at 4\u20137 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf hpf 2 hpf 4 hpf and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo 6hpf rep1", "GSM8147862", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:6hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo 6hpf rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:6hpf|genotype:AB TF and TLF", "GSM8147862", "GSM8147862: Zebrafish Embryo 6hpf rep1; Danio rerio; RNA Seq", "GSM8147862 r1", "GSM8147862", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_6hpf_1.fastq", "fastq", 1692395056.0, 22268356.0, "GSM8147862 r1", "0:76", "A:405083232;C:422494465;G:399989698;T:464749904;N:77757", 76, null, null, null, 405083232, 422494465, 399989698, 464749904, 77757, "SRX23954965", "SRS20755386", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31582, "SRR28471046", "SRX24073987", "SRS20864375", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 28", "GSM8171965", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 28", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171965", "GSM8171965: S10 slice 28; Danio rerio; RNA Seq", "GSM8171965 r1", "GSM8171965", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_28-R1.fq.gz S10_2_28-R2.fq.gz", "fastq fastq", 759288186.0, 2615807.0, "GSM8171965 r1", "0:143.73 1:146.54", "A:205364809;C:175246978;G:163844785;T:214825556;N:6058", 143, 146, null, null, 205364809, 175246978, 163844785, 214825556, 6058, "SRX24073987", "SRS20864375", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31583, "SRR28471047", "SRX24073986", "SRS20864377", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 27", "GSM8171964", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 27", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171964", "GSM8171964: S10 slice 27; Danio rerio; RNA Seq", "GSM8171964 r1", "GSM8171964", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_27-R1.fq.gz S10_2_27-R2.fq.gz", "fastq fastq", 6581985394.0, 22700834.0, "GSM8171964 r1", "0:143.52 1:146.42", "A:1794301951;C:1513541111;G:1430119165;T:1844015897;N:7270", 143, 146, null, null, 1794301951, 1513541111, 1430119165, 1844015897, 7270, "SRX24073986", "SRS20864377", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31584, "SRR28471048", "SRX24073985", "SRS20864373", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 26", "GSM8171962", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 26", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171962", "GSM8171962: S10 slice 26; Danio rerio; RNA Seq", "GSM8171962 r1", "GSM8171962", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_26-R1.fq.gz S10_2_26-R2.fq.gz", "fastq fastq", 7222374349.0, 24651582.0, "GSM8171962 r1", "0:145.51 1:147.47", "A:1979954857;C:1642503990;G:1569784440;T:2030123197;N:7865", 145, 147, null, null, 1979954857, 1642503990, 1569784440, 2030123197, 7865, "SRX24073985", "SRS20864373", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31585, "SRR28471049", "SRX24073984", "SRS20864374", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 25", "GSM8171961", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 25", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171961", "GSM8171961: S10 slice 25; Danio rerio; RNA Seq", "GSM8171961 r1", "GSM8171961", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_25-R1.fq.gz S10_2_25-R2.fq.gz", "fastq fastq", 6912437288.0, 23704050.0, "GSM8171961 r1", "0:144.17 1:147.45", "A:1886377008;C:1583136289;G:1524973541;T:1917942644;N:7806", 144, 147, null, null, 1886377008, 1583136289, 1524973541, 1917942644, 7806, "SRX24073984", "SRS20864374", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31586, "SRR28471050", "SRX24073983", "SRS20864372", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 24", "GSM8171960", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 24", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171960", "GSM8171960: S10 slice 24; Danio rerio; RNA Seq", "GSM8171960 r1", "GSM8171960", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_24-R1.fq.gz S10_2_24-R2.fq.gz", "fastq fastq", 6839477961.0, 23381494.0, "GSM8171960 r1", "0:145.10 1:147.42", "A:1878952639;C:1564093766;G:1477542759;T:1918881626;N:7171", 145, 147, null, null, 1878952639, 1564093766, 1477542759, 1918881626, 7171, "SRX24073983", "SRS20864372", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31587, "SRR28471051", "SRX24073982", "SRS20864371", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 23", "GSM8171959", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 23", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171959", "GSM8171959: S10 slice 23; Danio rerio; RNA Seq", "GSM8171959 r1", "GSM8171959", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_23-R1.fq.gz S10_2_23-R2.fq.gz", "fastq fastq", 7167273237.0, 24443101.0, "GSM8171959 r1", "0:145.85 1:147.38", "A:1939464339;C:1670904264;G:1550365240;T:2006531554;N:7840", 145, 147, null, null, 1939464339, 1670904264, 1550365240, 2006531554, 7840, "SRX24073982", "SRS20864371", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31588, "SRR28471052", "SRX24073981", "SRS20864369", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 22", "GSM8171958", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 22", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171958", "GSM8171958: S10 slice 22; Danio rerio; RNA Seq", "GSM8171958 r1", "GSM8171958", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_22-R1.fq.gz S10_2_22-R2.fq.gz", "fastq fastq", 7201833997.0, 24595383.0, "GSM8171958 r1", "0:145.55 1:147.26", "A:1961492345;C:1657551460;G:1566181731;T:2016600464;N:7997", 145, 147, null, null, 1961492345, 1657551460, 1566181731, 2016600464, 7997, "SRX24073981", "SRS20864369", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31589, "SRR28471053", "SRX24073980", "SRS20864370", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 21", "GSM8171957", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 21", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171957", "GSM8171957: S10 slice 21; Danio rerio; RNA Seq", "GSM8171957 r1", "GSM8171957", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_21-R1.fq.gz S10_2_21-R2.fq.gz", "fastq fastq", 7200671307.0, 24658175.0, "GSM8171957 r1", "0:145.00 1:147.02", "A:1952177571;C:1673984272;G:1548414880;T:2026087466;N:7118", 145, 147, null, null, 1952177571, 1673984272, 1548414880, 2026087466, 7118, "SRX24073980", "SRS20864370", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31590, "SRR28471054", "SRX24073979", "SRS20864368", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 20", "GSM8171955", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 20", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171955", "GSM8171955: S10 slice 20; Danio rerio; RNA Seq", "GSM8171955 r1", "GSM8171955", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_20-R1.fq.gz S10_2_20-R2.fq.gz", "fastq fastq", 7029384198.0, 24038713.0, "GSM8171955 r1", "0:145.27 1:147.15", "A:1927499291;C:1610291489;G:1509165690;T:1982420962;N:6766", 145, 147, null, null, 1927499291, 1610291489, 1509165690, 1982420962, 6766, "SRX24073979", "SRS20864368", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31591, "SRR28471055", "SRX24073978", "SRS20864367", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 19", "GSM8171954", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 19", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171954", "GSM8171954: S10 slice 19; Danio rerio; RNA Seq", "GSM8171954 r1", "GSM8171954", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_19-R1.fq.gz S10_2_19-R2.fq.gz", "fastq fastq", 6805088018.0, 23209224.0, "GSM8171954 r1", "0:145.80 1:147.41", "A:1868791398;C:1559085219;G:1478313464;T:1898890630;N:7307", 145, 147, null, null, 1868791398, 1559085219, 1478313464, 1898890630, 7307, "SRX24073978", "SRS20864367", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31592, "SRR28471056", "SRX24073977", "SRS20864366", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 18", "GSM8171953", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 18", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171953", "GSM8171953: S10 slice 18; Danio rerio; RNA Seq", "GSM8171953 r1", "GSM8171953", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_18-R1.fq.gz S10_2_18-R2.fq.gz", "fastq fastq", 6840069197.0, 23337475.0, "GSM8171953 r1", "0:145.70 1:147.40", "A:1857694353;C:1583014737;G:1489270628;T:1910082435;N:7044", 145, 147, null, null, 1857694353, 1583014737, 1489270628, 1910082435, 7044, "SRX24073977", "SRS20864366", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31593, "SRR28471057", "SRX24073976", "SRS20864365", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 17", "GSM8171952", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 17", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171952", "GSM8171952: S10 slice 17; Danio rerio; RNA Seq", "GSM8171952 r1", "GSM8171952", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_17-R1.fq.gz S10_2_17-R2.fq.gz", "fastq fastq", 6920104661.0, 23694104.0, "GSM8171952 r1", "0:144.63 1:147.43", "A:1895394336;C:1588574995;G:1506257815;T:1929870647;N:6868", 144, 147, null, null, 1895394336, 1588574995, 1506257815, 1929870647, 6868, "SRX24073976", "SRS20864365", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31594, "SRR28471058", "SRX24073975", "SRS20864364", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 16", "GSM8171951", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 16", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171951", "GSM8171951: S10 slice 16; Danio rerio; RNA Seq", "GSM8171951 r1", "GSM8171951", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_16-R1.fq.gz S10_2_16-R2.fq.gz", "fastq fastq", 6748107198.0, 22948597.0, "GSM8171951 r1", "0:146.16 1:147.89", "A:1844409884;C:1544282793;G:1510494929;T:1848854189;N:65403", 146, 147, null, null, 1844409884, 1544282793, 1510494929, 1848854189, 65403, "SRX24073975", "SRS20864364", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31595, "SRR28471059", "SRX24073974", "SRS20864362", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 15", "GSM8171950", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 15", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171950", "GSM8171950: S10 slice 15; Danio rerio; RNA Seq", "GSM8171950 r1", "GSM8171950", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_15-R1.fq.gz S10_2_15-R2.fq.gz", "fastq fastq", 7112483797.0, 24158094.0, "GSM8171950 r1", "0:146.51 1:147.90", "A:1947380194;C:1626263754;G:1557093148;T:1981676325;N:70376", 146, 147, null, null, 1947380194, 1626263754, 1557093148, 1981676325, 70376, "SRX24073974", "SRS20864362", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31596, "SRR28471060", "SRX24073973", "SRS20864363", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 14", "GSM8171949", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 14", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171949", "GSM8171949: S10 slice 14; Danio rerio; RNA Seq", "GSM8171949 r1", "GSM8171949", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_14-R1.fq.gz S10_2_14-R2.fq.gz", "fastq fastq", 7080198759.0, 24077121.0, "GSM8171949 r1", "0:146.28 1:147.78", "A:1936619266;C:1612882682;G:1571580901;T:1959049716;N:66194", 146, 147, null, null, 1936619266, 1612882682, 1571580901, 1959049716, 66194, "SRX24073973", "SRS20864363", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31597, "SRR28471061", "SRX24073972", "SRS20864361", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 13", "GSM8171948", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 13", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171948", "GSM8171948: S10 slice 13; Danio rerio; RNA Seq", "GSM8171948 r1", "GSM8171948", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_13-R1.fq.gz S10_2_13-R2.fq.gz", "fastq fastq", 6747408559.0, 22994643.0, "GSM8171948 r1", "0:145.81 1:147.62", "A:1853195990;C:1533549967;G:1475426554;T:1885166291;N:69757", 145, 147, null, null, 1853195990, 1533549967, 1475426554, 1885166291, 69757, "SRX24073972", "SRS20864361", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31598, "SRR28471062", "SRX24073971", "SRS20864360", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 12", "GSM8171947", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 12", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171947", "GSM8171947: S10 slice 12; Danio rerio; RNA Seq", "GSM8171947 r1", "GSM8171947", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_12-R1.fq.gz S10_2_12-R2.fq.gz", "fastq fastq", 6754504757.0, 22998351.0, "GSM8171947 r1", "0:145.99 1:147.70", "A:1834791847;C:1553263061;G:1499345250;T:1867038573;N:66026", 145, 147, null, null, 1834791847, 1553263061, 1499345250, 1867038573, 66026, "SRX24073971", "SRS20864360", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31599, "SRR28471063", "SRX24073970", "SRS20864359", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 11", "GSM8171946", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 11", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171946", "GSM8171946: S10 slice 11; Danio rerio; RNA Seq", "GSM8171946 r1", "GSM8171946", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_11-R1.fq.gz S10_2_11-R2.fq.gz", "fastq fastq", 7076755000.0, 24096043.0, "GSM8171946 r1", "0:146.07 1:147.62", "A:1941252061;C:1613847735;G:1571760406;T:1949829140;N:65658", 146, 147, null, null, 1941252061, 1613847735, 1571760406, 1949829140, 65658, "SRX24073970", "SRS20864359", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31600, "SRR28471064", "SRX24073969", "SRS20864358", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 10", "GSM8171945", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 10", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171945", "GSM8171945: S10 slice 10; Danio rerio; RNA Seq", "GSM8171945 r1", "GSM8171945", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_10-R1.fq.gz S10_2_10-R2.fq.gz", "fastq fastq", 7221414729.0, 24523966.0, "GSM8171945 r1", "0:146.41 1:148.05", "A:1978693512;C:1645520073;G:1593177021;T:2003957468;N:66655", 146, 148, null, null, 1978693512, 1645520073, 1593177021, 2003957468, 66655, "SRX24073969", "SRS20864358", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31601, "SRR28471065", "SRX24073968", "SRS20864357", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 9", "GSM8171943", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 9", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171943", "GSM8171943: S10 slice 9; Danio rerio; RNA Seq", "GSM8171943 r1", "GSM8171943", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_09-R1.fq.gz S10_2_09-R2.fq.gz", "fastq fastq", 7079443444.0, 24147001.0, "GSM8171943 r1", "0:145.21 1:147.97", "A:1943181435;C:1612981815;G:1577366874;T:1945843800;N:69520", 145, 147, null, null, 1943181435, 1612981815, 1577366874, 1945843800, 69520, "SRX24073968", "SRS20864357", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31602, "SRR28471066", "SRX24073967", "SRS20864356", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 8", "GSM8171942", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 8", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171942", "GSM8171942: S10 slice 8; Danio rerio; RNA Seq", "GSM8171942 r1", "GSM8171942", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_08-R1.fq.gz S10_2_08-R2.fq.gz", "fastq fastq", 7415196094.0, 25194114.0, "GSM8171942 r1", "0:146.01 1:148.31", "A:2024066191;C:1698099791;G:1663826446;T:2029139484;N:64182", 146, 148, null, null, 2024066191, 1698099791, 1663826446, 2029139484, 64182, "SRX24073967", "SRS20864356", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31603, "SRR28471067", "SRX24073966", "SRS20864355", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 7", "GSM8171941", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 7", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171941", "GSM8171941: S10 slice 7; Danio rerio; RNA Seq", "GSM8171941 r1", "GSM8171941", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_07-R1.fq.gz S10_2_07-R2.fq.gz", "fastq fastq", 6928839764.0, 23504899.0, "GSM8171941 r1", "0:146.77 1:148.01", "A:1887104011;C:1594417798;G:1528216585;T:1919032199;N:69171", 146, 148, null, null, 1887104011, 1594417798, 1528216585, 1919032199, 69171, "SRX24073966", "SRS20864355", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31604, "SRR28471068", "SRX24073965", "SRS20864353", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 6", "GSM8171940", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 6", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171940", "GSM8171940: S10 slice 6; Danio rerio; RNA Seq", "GSM8171940 r1", "GSM8171940", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_06-R1.fq.gz S10_2_06-R2.fq.gz", "fastq fastq", 6941276864.0, 23612146.0, "GSM8171940 r1", "0:146.22 1:147.75", "A:1914736932;C:1565697792;G:1520746150;T:1940028982;N:67008", 146, 147, null, null, 1914736932, 1565697792, 1520746150, 1940028982, 67008, "SRX24073965", "SRS20864353", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31605, "SRR28471069", "SRX24073964", "SRS20864354", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 5", "GSM8171939", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 5", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171939", "GSM8171939: S10 slice 5; Danio rerio; RNA Seq", "GSM8171939 r1", "GSM8171939", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_05-R1.fq.gz S10_2_05-R2.fq.gz", "fastq fastq", 6764562925.0, 23007531.0, "GSM8171939 r1", "0:146.31 1:147.71", "A:1843213356;C:1551510075;G:1502733012;T:1867039161;N:67321", 146, 147, null, null, 1843213356, 1551510075, 1502733012, 1867039161, 67321, "SRX24073964", "SRS20864354", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31606, "SRR28471070", "SRX24073963", "SRS20864352", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 4", "GSM8171938", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 4", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171938", "GSM8171938: S10 slice 4; Danio rerio; RNA Seq", "GSM8171938 r1", "GSM8171938", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_04-R1.fq.gz S10_2_04-R2.fq.gz", "fastq fastq", 7344067889.0, 24926409.0, "GSM8171938 r1", "0:146.67 1:147.96", "A:1987383092;C:1697428868;G:1643668260;T:2015515691;N:71978", 146, 147, null, null, 1987383092, 1697428868, 1643668260, 2015515691, 71978, "SRX24073963", "SRS20864352", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31607, "SRR28471071", "SRX24073962", "SRS20864351", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 3", "GSM8171937", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171937", "GSM8171937: S10 slice 3; Danio rerio; RNA Seq", "GSM8171937 r1", "GSM8171937", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_03-R1.fq.gz S10_2_03-R2.fq.gz", "fastq fastq", 7363849831.0, 24981769.0, "GSM8171937 r1", "0:146.81 1:147.96", "A:1996759015;C:1702083886;G:1660658214;T:2004280097;N:68619", 146, 147, null, null, 1996759015, 1702083886, 1660658214, 2004280097, 68619, "SRX24073962", "SRS20864351", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31608, "SRR28471072", "SRX24073961", "SRS20864350", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 2", "GSM8171936", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171936", "GSM8171936: S10 slice 2; Danio rerio; RNA Seq", "GSM8171936 r1", "GSM8171936", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_02-R1.fq.gz S10_2_02-R2.fq.gz", "fastq fastq", 6931685121.0, 23498952.0, "GSM8171936 r1", "0:146.85 1:148.13", "A:1873586789;C:1604107934;G:1559935625;T:1893983444;N:71329", 146, 148, null, null, 1873586789, 1604107934, 1559935625, 1893983444, 71329, "SRX24073961", "SRS20864350", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31609, "SRR28471073", "SRX24073960", "SRS20864349", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.", null, null, null, "S10 slice 1", "GSM8171935", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing", "S10 slice 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:10 hpf", "GSM8171935", "GSM8171935: S10 slice 1; Danio rerio; RNA Seq", "GSM8171935 r1", "GSM8171935", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S10_2_01-R1.fq.gz S10_2_01-R2.fq.gz", "fastq fastq", 6843352152.0, 23814595.0, "GSM8171935 r1", "0:141.43 1:145.93", "A:1790832238;C:1645937440;G:1595226694;T:1811285453;N:70327", 141, 145, null, null, 1790832238, 1645937440, 1595226694, 1811285453, 70327, "SRX24073960", "SRS20864349", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42249, "SRR5507584", "SRX2783295", "SRS2165432", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 14", "GSM2598411", null, "tissue:F1 embryos from exposed parents 8.7 mGy/h post 1y|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 14", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 8.7 mGy/h post 1y", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598411", "GSM2598411: Nmbu RNA 14; Danio rerio; RNA Seq", "GSM2598411", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598411", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-14_HL7MMCCXX_L4_1.fq.gz nmbu-RNA-14_HL7MMCCXX_L4_2.fq.gz", "fastq fastq", 5633328900.0, 18777763.0, "GSM2598411 r1", "0:150 1:150", "A:1412757538;C:1395215147;G:1427182503;T:1397831592;N:342120", 150, 150, null, null, 1412757538, 1395215147, 1427182503, 1397831592, 342120, "SRX2783295", "SRS2165432", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.95017, 0.94647, 0.05539, 0.05499, 0.75556, 0.75952, 0.50736, 0.51408, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42250, "SRR5507583", "SRX2783294", "SRS2165431", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 13", "GSM2598410", null, "tissue:F1 embryos from exposed parents 8.7 mGy/h post 1y|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 13", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 8.7 mGy/h post 1y", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598410", "GSM2598410: Nmbu RNA 13; Danio rerio; RNA Seq", "GSM2598410", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598410", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-13_HL7MMCCXX_L7_2.fq.gz nmbu-RNA-13_HL7MMCCXX_L7_1.fq.gz", "fastq fastq", 5599755900.0, 18665853.0, "GSM2598410 r1", "0:150 1:150", "A:1404620725;C:1387199335;G:1416438941;T:1391401113;N:95786", 150, 150, null, null, 1404620725, 1387199335, 1416438941, 1391401113, 95786, "SRX2783294", "SRS2165431", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.93657, 0.9336, 0.05248, 0.05297, 0.75976, 0.76341, 0.5058, 0.51203, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42251, "SRR5507582", "SRX2783293", "SRS2165430", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 12", "GSM2598409", null, "tissue:F1 embryos from exposed parents 8.7 mGy/h post 1y|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 12", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 8.7 mGy/h post 1y", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598409", "GSM2598409: Nmbu RNA 12; Danio rerio; RNA Seq", "GSM2598409", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598409", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-12_HL7MMCCXX_L7_1.fq.gz nmbu-RNA-12_HL7MMCCXX_L7_2.fq.gz", "fastq fastq", 4952161800.0, 16507206.0, "GSM2598409 r1", "0:150 1:150", "A:1230899823;C:1237646178;G:1266394880;T:1217138000;N:82919", 150, 150, null, null, 1230899823, 1237646178, 1266394880, 1217138000, 82919, "SRX2783293", "SRS2165430", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.93788, 0.91885, 0.05143, 0.05069, 0.75696, 0.76152, 0.50037, 0.5117, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42252, "SRR5507581", "SRX2783292", "SRS2165429", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 11", "GSM2598408", null, "tissue:F1 embryos from non exposed parents post 1y|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 11", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from non exposed parents post 1y", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598408", "GSM2598408: Nmbu RNA 11; Danio rerio; RNA Seq", "GSM2598408", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598408", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-11_HL7MMCCXX_L7_1.fq.gz nmbu-RNA-11_HL7MMCCXX_L7_2.fq.gz", "fastq fastq", 4237648200.0, 14125494.0, "GSM2598408 r1", "0:150 1:150", "A:1056844676;C:1054623496;G:1077647873;T:1048459873;N:72282", 150, 150, null, null, 1056844676, 1054623496, 1077647873, 1048459873, 72282, "SRX2783292", "SRS2165429", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94244, 0.94606, 0.04758, 0.04771, 0.75254, 0.75578, 0.50378, 0.50499, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42253, "SRR5507580", "SRX2783291", "SRS2165428", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 10", "GSM2598407", null, "tissue:F1 embryos from non exposed parents 1y later|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 10", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from non exposed parents 1y later", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598407", "GSM2598407: Nmbu RNA 10; Danio rerio; RNA Seq", "GSM2598407", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598407", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-10_HL7MMCCXX_L8_1.fq.gz nmbu-RNA-10_HL7MMCCXX_L8_2.fq.gz", "fastq fastq", 4963104900.0, 16543683.0, "GSM2598407 r1", "0:150 1:150", "A:1235094134;C:1237803645;G:1264868074;T:1224620276;N:718771", 150, 150, null, null, 1235094134, 1237803645, 1264868074, 1224620276, 718771, "SRX2783291", "SRS2165428", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94253, 0.94276, 0.05189, 0.0515, 0.75519, 0.76272, 0.50647, 0.50429, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42254, "SRR5507579", "SRX2783290", "SRS2165427", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 9", "GSM2598406", null, "tissue:F1 embryos from non exposed parents 1y later|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 9", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from non exposed parents 1y later", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598406", "GSM2598406: Nmbu RNA 9; Danio rerio; RNA Seq", "GSM2598406", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598406", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-9_HL7MMCCXX_L8_1.fq.gz nmbu-RNA-9_HL7MMCCXX_L8_2.fq.gz", "fastq fastq", 6023150100.0, 20077167.0, "GSM2598406 r1", "0:150 1:150", "A:1498133065;C:1504764333;G:1537232736;T:1482144144;N:875822", 150, 150, null, null, 1498133065, 1504764333, 1537232736, 1482144144, 875822, "SRX2783290", "SRS2165427", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94291, 0.94229, 0.05033, 0.05039, 0.75477, 0.76179, 0.50732, 0.50859, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42255, "SRR5507578", "SRX2783289", "SRS2165426", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 8", "GSM2598405", null, "tissue:F1 embryos from non exposed parents|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 8", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from non exposed parents", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598405", "GSM2598405: Nmbu RNA 8; Danio rerio; RNA Seq", "GSM2598405", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598405", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-8_HL7MMCCXX_L8_2.fq.gz nmbu-RNA-8_HL7MMCCXX_L8_1.fq.gz", "fastq fastq", 6415521600.0, 21385072.0, "GSM2598405 r1", "0:150 1:150", "A:1649576625;C:1546068135;G:1579782334;T:1639155192;N:939314", 150, 150, null, null, 1649576625, 1546068135, 1579782334, 1639155192, 939314, "SRX2783289", "SRS2165426", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.93889, 0.93814, 0.05068, 0.05014, 0.73799, 0.7456, 0.47327, 0.48312, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42256, "SRR5507577", "SRX2783288", "SRS2165425", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 7", "GSM2598404", null, "tissue:F1 embryos from non exposed parents|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 7", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from non exposed parents", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598404", "GSM2598404: Nmbu RNA 7; Danio rerio; RNA Seq", "GSM2598404", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598404", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-7_HL7MMCCXX_L8_1.fq.gz nmbu-RNA-7_HL7MMCCXX_L8_2.fq.gz", "fastq fastq", 5608012200.0, 18693374.0, "GSM2598404 r1", "0:150 1:150", "A:1415857301;C:1377843946;G:1410729794;T:1402785996;N:795163", 150, 150, null, null, 1415857301, 1377843946, 1410729794, 1402785996, 795163, "SRX2783288", "SRS2165425", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94088, 0.94009, 0.03763, 0.03726, 0.74659, 0.75329, 0.48064, 0.47991, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42257, "SRR5507576", "SRX2783287", "SRS2165424", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 6", "GSM2598403", null, "tissue:F1 embryos from exposed parents 53 mGy/h|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 6", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 53 mGy/h", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598403", "GSM2598403: Nmbu RNA 6; Danio rerio; RNA Seq", "GSM2598403", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598403", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-6_HL7MMCCXX_L5_2.fq.gz nmbu-RNA-6_HL7MMCCXX_L5_1.fq.gz", "fastq fastq", 5495224800.0, 18317416.0, "GSM2598403 r1", "0:150 1:150", "A:1396538260;C:1340395983;G:1374759921;T:1383194558;N:336078", 150, 150, null, null, 1396538260, 1340395983, 1374759921, 1383194558, 336078, "SRX2783287", "SRS2165424", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.93426, 0.93342, 0.02553, 0.0253, 0.7487, 0.75126, 0.48364, 0.48279, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42258, "SRR5507575", "SRX2783286", "SRS2165423", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 5", "GSM2598402", null, "tissue:F1 embryos from exposed parents 53 mGy/h|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 5", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 53 mGy/h", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598402", "GSM2598402: Nmbu RNA 5; Danio rerio; RNA Seq", "GSM2598402", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598402", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-5_HL7MMCCXX_L8_1.fq.gz nmbu-RNA-5_HL7MMCCXX_L8_2.fq.gz", "fastq fastq", 5791636800.0, 19305456.0, "GSM2598402 r1", "0:150 1:150", "A:1450364496;C:1432531988;G:1467067536;T:1440859423;N:813357", 150, 150, null, null, 1450364496, 1432531988, 1467067536, 1440859423, 813357, "SRX2783286", "SRS2165423", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94159, 0.94537, 0.02156, 0.02156, 0.75682, 0.76327, 0.47844, 0.47169, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42259, "SRR5507574", "SRX2783285", "SRS2165421", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 4", "GSM2598401", null, "tissue:F1 embryos from exposed parents 53 mGy/h|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 4", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 53 mGy/h", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598401", "GSM2598401: Nmbu RNA 4; Danio rerio; RNA Seq", "GSM2598401", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598401", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-4_HL7MMCCXX_L6_2.fq.gz nmbu-RNA-4_HL7MMCCXX_L6_1.fq.gz", "fastq fastq", 5954300100.0, 19847667.0, "GSM2598401 r1", "0:150 1:150", "A:1519090741;C:1447646085;G:1482495589;T:1504622376;N:445309", 150, 150, null, null, 1519090741, 1447646085, 1482495589, 1504622376, 445309, "SRX2783285", "SRS2165421", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94155, 0.93672, 0.02741, 0.02718, 0.75152, 0.7555, 0.48469, 0.48497, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42260, "SRR5507573", "SRX2783284", "SRS2165422", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 3", "GSM2598400", null, "tissue:F1 embryos from exposed parents 8.7 mGy/h|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 3", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 8.7 mGy/h", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598400", "GSM2598400: Nmbu RNA 3; Danio rerio; RNA Seq", "GSM2598400", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598400", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-3_HL7MMCCXX_L6_1.fq.gz nmbu-RNA-3_HL7MMCCXX_L6_2.fq.gz", "fastq fastq", 5198459700.0, 17328199.0, "GSM2598400 r1", "0:150 1:150", "A:1337776560;C:1254488044;G:1284401452;T:1321404044;N:389600", 150, 150, null, null, 1337776560, 1254488044, 1284401452, 1321404044, 389600, "SRX2783284", "SRS2165422", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94089, 0.93786, 0.03856, 0.03842, 0.74519, 0.74899, 0.47956, 0.48449, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42261, "SRR5507572", "SRX2783283", "SRS2165420", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 2", "GSM2598399", null, "tissue:F1 embryos from exposed parents 8.7 mGy/h|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 2", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 8.7 mGy/h", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598399", "GSM2598399: Nmbu RNA 2; Danio rerio; RNA Seq", "GSM2598399", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598399", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-2_HL7MMCCXX_L6_2.fq.gz nmbu-RNA-2_HL7MMCCXX_L6_1.fq.gz", "fastq fastq", 6078246300.0, 20260821.0, "GSM2598399 r1", "0:150 1:150", "A:1535292399;C:1491268720;G:1527779972;T:1523448305;N:456904", 150, 150, null, null, 1535292399, 1491268720, 1527779972, 1523448305, 456904, "SRX2783283", "SRS2165420", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.9423, 0.94156, 0.03814, 0.03775, 0.74602, 0.74894, 0.48729, 0.48831, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42262, "SRR5507571", "SRX2783282", "SRS2165419", "SRP106454", "PRJNA385396", "Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring", "GSE98539", "Transcriptome Analysis", "In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.", null, "pubmed:29248853;pubmed:33602989", null, "Nmbu RNA 1", "GSM2598398", null, "tissue:F1 embryos from exposed parents 8.7 mGy/h|strain:AB wild type|developmental stage:5.5 hpf", "Nmbu RNA 1", "Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.", "F1 embryos from exposed parents 8.7 mGy/h", "AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", null, "strain:AB wild type|developmental stage:5.5 hpf", "GSM2598398", "GSM2598398: Nmbu RNA 1; Danio rerio; RNA Seq", "GSM2598398", null, "1", "Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures\u2019 instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 \u00b5l RNase free water and stored at \u2212 80\u00b0C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 \u00b5g total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation\u2019s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.", "GEO Accession:GSM2598398", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP106454", null, null, "nmbu-RNA-1_HL7MMCCXX_L6_2.fq.gz nmbu-RNA-1_HL7MMCCXX_L6_1.fq.gz", "fastq fastq", 5353026600.0, 17843422.0, "GSM2598398 r1", "0:150 1:150", "A:1385801067;C:1283289927;G:1315186291;T:1368350896;N:398419", 150, 150, null, null, 1385801067, 1283289927, 1315186291, 1368350896, 398419, "SRX2783282", "SRS2165419", "SRA559556", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 2, 0.94212, 0.93997, 0.03935, 0.03931, 0.74403, 0.75053, 0.48308, 0.48777, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "Norway", "2017-05-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [47621, "SRR6784687", "SRX3744225", "SRS3000693", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here through genome wide profiling of RNA abundance and three prime modification we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus maternal mRNA clearance is significantly delayed leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7 with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets rs1a rs2b and rs2 were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 6 hpf whole embryo injected with TUT47MO Exp. ID: rs1b", "GSM3024079", null, "tissue:Zebrafish whole embryo|hpf translation blocking TUT7 translation blocking|strain:AB", "Zebrafish 6 hpf whole embryo injected with TUT47MO Exp. ID: rs1b", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking TUT7 translation blocking|strain:AB", "GSM3024079", "GSM3024079: Zebrafish 6 hpf whole embryo injected with TUT47MO Exp. ID: rs1b; Danio rerio; RNA Seq", "GSM3024079", null, "1", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "GEO Accession:GSM3024079", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1b-TUT47MO-6hpf_R1.fastq.gz rs1b-TUT47MO-6hpf_R2.fastq.gz", "fastq fastq", 3435241350.0, 22901609.0, "GSM3024079 r1", "0:75 1:75", "A:889477946;C:823042256;G:819721543;T:901155072;N:1844533", 75, 75, null, null, 889477946, 823042256, 819721543, 901155072, 1844533, "SRX3744225", "SRS3000693", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.93251, 0.93567, 0.16521, 0.16237, 0.72174, 0.72366, 0.50678, 0.50962, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47623, "SRR6784685", "SRX3744223", "SRS3000692", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here through genome wide profiling of RNA abundance and three prime modification we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus maternal mRNA clearance is significantly delayed leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7 with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets rs1a rs2b and rs2 were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 6 hpf whole embryo injected with ConMO Exp. ID: rs1b", "GSM3024077", null, "tissue:Zebrafish whole embryo|hpf", "Zebrafish 6 hpf whole embryo injected with ConMO Exp. ID: rs1b", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf", "GSM3024077", "GSM3024077: Zebrafish 6 hpf whole embryo injected with ConMO Exp. ID: rs1b; Danio rerio; RNA Seq", "GSM3024077", null, "1", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "GEO Accession:GSM3024077", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1b-ConMO-6hpf_R1.fastq.gz rs1b-ConMO-6hpf_R2.fastq.gz", "fastq fastq", 2983247100.0, 19888314.0, "GSM3024077 r1", "0:75 1:75", "A:788608401;C:697190406;G:697628856;T:798199246;N:1620191", 75, 75, null, null, 788608401, 697190406, 697628856, 798199246, 1620191, "SRX3744223", "SRS3000692", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.92959, 0.93349, 0.22106, 0.21943, 0.74065, 0.74414, 0.51047, 0.50898, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47625, "SRR6784683", "SRX3744221", "SRS3000690", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here through genome wide profiling of RNA abundance and three prime modification we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus maternal mRNA clearance is significantly delayed leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7 with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets rs1a rs2b and rs2 were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 6 hpf whole embryo injected with TUT47MO Exp. ID: rs1a", "GSM3024075", null, "tissue:Zebrafish whole embryo|hpf translation blocking TUT7 translation blocking|strain:AB", "Zebrafish 6 hpf whole embryo injected with TUT47MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking TUT7 translation blocking|strain:AB", "GSM3024075", "GSM3024075: Zebrafish 6 hpf whole embryo injected with TUT47MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024075", null, "1", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "GEO Accession:GSM3024075", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT47MO-6hpf_R2.fastq.gz rs1a-TUT47MO-6hpf_R1.fastq.gz", "fastq fastq", 4148426700.0, 27656178.0, "GSM3024075 r1", "0:75 1:75", "A:1116281930;C:955948003;G:947031316;T:1126881280;N:2284171", 75, 75, null, null, 1116281930, 955948003, 947031316, 1126881280, 2284171, "SRX3744221", "SRS3000690", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95744, 0.96413, 0.08802, 0.08672, 0.76706, 0.77053, 0.76514, 0.77071, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47628, "SRR6784680", "SRX3744218", "SRS3000687", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here through genome wide profiling of RNA abundance and three prime modification we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus maternal mRNA clearance is significantly delayed leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7 with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets rs1a rs2b and rs2 were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 6 hpf whole embryo injected with TUT7MO Exp. ID: rs1a", "GSM3024072", null, "tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB", "Zebrafish 6 hpf whole embryo injected with TUT7MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking|strain:AB", "GSM3024072", "GSM3024072: Zebrafish 6 hpf whole embryo injected with TUT7MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024072", null, "1", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "GEO Accession:GSM3024072", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT7MO-6hpf_R1.fastq.gz rs1a-TUT7MO-6hpf_R2.fastq.gz", "fastq fastq", 4210870200.0, 28072468.0, "GSM3024072 r1", "0:75 1:75", "A:1137162277;C:966672642;G:958012123;T:1146763336;N:2259822", 75, 75, null, null, 1137162277, 966672642, 958012123, 1146763336, 2259822, "SRX3744218", "SRS3000687", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.94795, 0.95515, 0.09408, 0.09277, 0.76786, 0.7721, 0.76029, 0.76033, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47631, "SRR6784677", "SRX3744215", "SRS3000684", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here through genome wide profiling of RNA abundance and three prime modification we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus maternal mRNA clearance is significantly delayed leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7 with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets rs1a rs2b and rs2 were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 6 hpf whole embryo injected with TUT4MO Exp. ID: rs1a", "GSM3024069", null, "tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB", "Zebrafish 6 hpf whole embryo injected with TUT4MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking|strain:AB", "GSM3024069", "GSM3024069: Zebrafish 6 hpf whole embryo injected with TUT4MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024069", null, "1", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "GEO Accession:GSM3024069", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT4MO-6hpf_R1.fastq.gz rs1a-TUT4MO-6hpf_R2.fastq.gz", "fastq fastq", 4111176450.0, 27407843.0, "GSM3024069 r1", "0:75 1:75", "A:1106216549;C:946715229;G:938053400;T:1117948899;N:2242373", 75, 75, null, null, 1106216549, 946715229, 938053400, 1117948899, 2242373, "SRX3744215", "SRS3000684", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95489, 0.96138, 0.09872, 0.09765, 0.77573, 0.77871, 0.74578, 0.74972, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47634, "SRR6784674", "SRX3744212", "SRS3000681", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here through genome wide profiling of RNA abundance and three prime modification we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus maternal mRNA clearance is significantly delayed leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7 with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets rs1a rs2b and rs2 were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 6 hpf whole embryo injected with ConMO Exp. ID: rs1a", "GSM3024066", null, "tissue:Zebrafish whole embryo|hpf", "Zebrafish 6 hpf whole embryo injected with ConMO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf", "GSM3024066", "GSM3024066: Zebrafish 6 hpf whole embryo injected with ConMO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024066", null, "1", "For each sample embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2 to yield paired end 76nt reads.", "GEO Accession:GSM3024066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-ConMO-6hpf_R2.fastq.gz rs1a-ConMO-6hpf_R1.fastq.gz", "fastq fastq", 7032009600.0, 46880064.0, "GSM3024066 r1", "0:75 1:75", "A:1895020787;C:1619030267;G:1602716135;T:1911373524;N:3868887", 75, 75, null, null, 1895020787, 1619030267, 1602716135, 1911373524, 3868887, "SRX3744212", "SRS3000681", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95375, 0.96018, 0.1127, 0.11091, 0.77733, 0.77887, 0.74785, 0.74951, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [56017, "SRR10836800", "SRX7508636", "SRS5949028", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Cyt", "GSM4252157", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "Shield Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "GSM4252157", "GSM4252157: Shield Cyt; Danio rerio; RNA Seq", "GSM4252157", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252157", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-C2_L001_R2_001.fastq.gz Shield-C2_L001_R1_001.fastq.gz", "fastq fastq", 1329331421.0, 8804641.0, "GSM4252157 r1", "0:75.56 1:75.43", "A:305005869;C:318506142;G:400124814;T:305276315;N:418281", 75, 75, null, null, 305005869, 318506142, 400124814, 305276315, 418281, "SRX7508636", "SRS5949028", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.84759, 0.83992, 0.09786, 0.09369, 0.78875, 0.79198, 0.65537, 0.65408, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56018, "SRR10836801", "SRX7508636", "SRS5949028", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Cyt", "GSM4252157", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "Shield Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "GSM4252157", "GSM4252157: Shield Cyt; Danio rerio; RNA Seq", "GSM4252157", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252157", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-C2_L002_R2_001.fastq.gz Shield-C2_L002_R1_001.fastq.gz", "fastq fastq", 1285409588.0, 8515701.0, "GSM4252157 r2", "0:75.53 1:75.41", "A:302650389;C:312196883;G:370947604;T:299160581;N:454131", 75, 75, null, null, 302650389, 312196883, 370947604, 299160581, 454131, "SRX7508636", "SRS5949028", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.84444, 0.83539, 0.0979, 0.09417, 0.78744, 0.79125, 0.66157, 0.65079, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56019, "SRR10836802", "SRX7508636", "SRS5949028", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Cyt", "GSM4252157", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "Shield Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "GSM4252157", "GSM4252157: Shield Cyt; Danio rerio; RNA Seq", "GSM4252157", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252157", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-C2_L003_R1_001.fastq.gz Shield-C2_L003_R2_001.fastq.gz", "fastq fastq", 1312869275.0, 8696752.0, "GSM4252157 r3", "0:75.54 1:75.43", "A:307673523;C:318217101;G:381874266;T:304950845;N:153540", 75, 75, null, null, 307673523, 318217101, 381874266, 304950845, 153540, "SRX7508636", "SRS5949028", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.844, 0.83842, 0.10021, 0.09501, 0.78762, 0.79113, 0.65574, 0.64806, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56020, "SRR10836803", "SRX7508636", "SRS5949028", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Cyt", "GSM4252157", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "Shield Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Cytosolic", "GSM4252157", "GSM4252157: Shield Cyt; Danio rerio; RNA Seq", "GSM4252157", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252157", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-C2_L004_R1_001.fastq.gz Shield-C2_L004_R2_001.fastq.gz", "fastq fastq", 1258856388.0, 8339500.0, "GSM4252157 r4", "0:75.53 1:75.42", "A:300940054;C:312735416;G:347004073;T:297990805;N:186040", 75, 75, null, null, 300940054, 312735416, 347004073, 297990805, 186040, "SRX7508636", "SRS5949028", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.83965, 0.83365, 0.09713, 0.09352, 0.78744, 0.79093, 0.65822, 0.66127, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56021, "SRR10836796", "SRX7508635", "SRS5949027", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Nuc", "GSM4252156", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "Shield Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "GSM4252156", "GSM4252156: Shield Nuc; Danio rerio; RNA Seq", "GSM4252156", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252156", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-N2_L001_R1_001.fastq.gz Shield-N2_L001_R2_001.fastq.gz", "fastq fastq", 1782370230.0, 11806788.0, "GSM4252156 r1", "0:75.51 1:75.46", "A:501150025;C:371861852;G:399693603;T:509119681;N:545069", 75, 75, null, null, 501150025, 371861852, 399693603, 509119681, 545069, "SRX7508635", "SRS5949027", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.88781, 0.88767, 0.50682, 0.5034, 0.7553, 0.76015, 0.58201, 0.43076, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56022, "SRR10836797", "SRX7508635", "SRS5949027", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Nuc", "GSM4252156", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "Shield Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "GSM4252156", "GSM4252156: Shield Nuc; Danio rerio; RNA Seq", "GSM4252156", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252156", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-N2_L002_R1_001.fastq.gz Shield-N2_L002_R2_001.fastq.gz", "fastq fastq", 1733341704.0, 11482905.0, "GSM4252156 r2", "0:75.50 1:75.45", "A:490206078;C:362602859;G:383328293;T:496631424;N:573050", 75, 75, null, null, 490206078, 362602859, 383328293, 496631424, 573050, "SRX7508635", "SRS5949027", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.88714, 0.88815, 0.50524, 0.50249, 0.75657, 0.75962, 0.58676, 0.58432, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56023, "SRR10836798", "SRX7508635", "SRS5949027", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Nuc", "GSM4252156", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "Shield Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "GSM4252156", "GSM4252156: Shield Nuc; Danio rerio; RNA Seq", "GSM4252156", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252156", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-N2_L003_R1_001.fastq.gz Shield-N2_L003_R2_001.fastq.gz", "fastq fastq", 1765519865.0, 11694748.0, "GSM4252156 r3", "0:75.50 1:75.46", "A:498798048;C:369308691;G:391592420;T:505641214;N:179492", 75, 75, null, null, 498798048, 369308691, 391592420, 505641214, 179492, "SRX7508635", "SRS5949027", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.8876, 0.88757, 0.50629, 0.50456, 0.75532, 0.76187, 0.58163, 0.43324, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56024, "SRR10836799", "SRX7508635", "SRS5949027", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell 256 Cell 1000 Cell Dome and Shield stages of development.", null, "pubmed:33795334", null, "Shield Nuc", "GSM4252156", null, "source name:Shield stage embryo|tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "Shield Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Shield stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell 256 cell 1000 cell shield 24hpf 50hpf. The embryos were treated with Pronase protease from Streptomyces griseus Sigma Aldrich to remove the chorion 1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Shield|fraction:Nuclear", "GSM4252156", "GSM4252156: Shield Nuc; Danio rerio; RNA Seq", "GSM4252156", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252156", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Shield-N2_L004_R1_001.fastq.gz Shield-N2_L004_R2_001.fastq.gz", "fastq fastq", 1719275634.0, 11389011.0, "GSM4252156 r4", "0:75.50 1:75.46", "A:487926938;C:360717008;G:376046730;T:494361645;N:223313", 75, 75, null, null, 487926938, 360717008, 376046730, 494361645, 223313, "SRX7508635", "SRS5949027", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.88634, 0.88888, 0.50268, 0.5033, 0.75657, 0.76002, 0.58518, 0.43388, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62993, "SRR13565182", "SRX9963426", "SRS8137093", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep3", "GSM5047610", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA and treated with CHX", "zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep3", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA and treated with CHX", "GSM5047610", "GSM5047610: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep3; Danio rerio; RNA Seq", "GSM5047610", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047610", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_chx_6h_3_FRAS190066757-1a_1.clean.fq.gz wt_cyc_chx_6h_3_FRAS190066757-1a_2.clean.fq.gz", "fastq fastq", 9002426400.0, 30008088.0, "GSM5047610 r1", "0:150 1:150", "A:2380778541;C:2132007664;G:2141040035;T:2348500151;N:100009", 150, 150, null, null, 2380778541, 2132007664, 2141040035, 2348500151, 100009, "SRX9963426", "SRS8137093", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95265, 0.95206, 0.05931, 0.05981, 0.73882, 0.73979, 0.48229, 0.48066, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62994, "SRR13565181", "SRX9963425", "SRS8137092", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep2", "GSM5047609", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA and treated with CHX", "zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep2", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA and treated with CHX", "GSM5047609", "GSM5047609: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep2; Danio rerio; RNA Seq", "GSM5047609", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047609", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_chx_6h_2_FRAS190066756-1a_1.clean.fq.gz wt_cyc_chx_6h_2_FRAS190066756-1a_2.clean.fq.gz", "fastq fastq", 7507488000.0, 25024960.0, "GSM5047609 r1", "0:150 1:150", "A:1983050893;C:1781485586;G:1786404896;T:1956460578;N:86047", 150, 150, null, null, 1983050893, 1781485586, 1786404896, 1956460578, 86047, "SRX9963425", "SRS8137092", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95238, 0.95206, 0.05548, 0.05559, 0.73659, 0.73787, 0.48168, 0.47976, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62995, "SRR13565180", "SRX9963424", "SRS8137091", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep1", "GSM5047608", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA and treated with CHX", "zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep1", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA and treated with CHX", "GSM5047608", "GSM5047608: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep1; Danio rerio; RNA Seq", "GSM5047608", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047608", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_chx_6h_1_FRAS190066755-1a_1.clean.fq.gz wt_cyc_chx_6h_1_FRAS190066755-1a_2.clean.fq.gz", "fastq fastq", 8600280000.0, 28667600.0, "GSM5047608 r1", "0:150 1:150", "A:2278632082;C:2034644513;G:2039749820;T:2247156598;N:96987", 150, 150, null, null, 2278632082, 2034644513, 2039749820, 2247156598, 96987, "SRX9963424", "SRS8137091", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95179, 0.95024, 0.05267, 0.05208, 0.74205, 0.7418, 0.47917, 0.48101, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63002, "SRR13565173", "SRX9963417", "SRS8137084", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep3", "GSM5047601", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA", "zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep3", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA", "GSM5047601", "GSM5047601: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep3; Danio rerio; RNA Seq", "GSM5047601", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047601", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_50_6h_3_FRAS190066754-1a_1.clean.fq.gz wt_cyc_50_6h_3_FRAS190066754-1a_2.clean.fq.gz", "fastq fastq", 8242659000.0, 27475530.0, "GSM5047601 r1", "0:150 1:150", "A:2192023477;C:1945136462;G:1952531616;T:2152873603;N:93842", 150, 150, null, null, 2192023477, 1945136462, 1952531616, 2152873603, 93842, "SRX9963417", "SRS8137084", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95285, 0.95124, 0.07112, 0.07074, 0.75645, 0.75795, 0.46618, 0.46678, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63003, "SRR13565172", "SRX9963416", "SRS8137083", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2", "GSM5047600", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA", "zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA", "GSM5047600", "GSM5047600: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2; Danio rerio; RNA Seq", "GSM5047600", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047600", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_50_6h_2_FRAS190066753-1a_1.clean.fq.gz wt_cyc_50_6h_2_FRAS190066753-1a_2.clean.fq.gz", "fastq fastq", 8468408100.0, 28228027.0, "GSM5047600 r1", "0:150 1:150", "A:2252327754;C:1995087946;G:2004951478;T:2215944168;N:96754", 150, 150, null, null, 2252327754, 1995087946, 2004951478, 2215944168, 96754, "SRX9963416", "SRS8137083", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95119, 0.94983, 0.06689, 0.06701, 0.76404, 0.76469, 0.47462, 0.47055, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63004, "SRR13565171", "SRX9963415", "SRS8137082", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep1", "GSM5047599", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA", "zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep1", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA", "GSM5047599", "GSM5047599: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep1; Danio rerio; RNA Seq", "GSM5047599", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047599", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_50_6h_1_FRAS190066752-1a_1.clean.fq.gz wt_cyc_50_6h_1_FRAS190066752-1a_2.clean.fq.gz", "fastq fastq", 8053099500.0, 26843665.0, "GSM5047599 r1", "0:150 1:150", "A:2143298124;C:1896537115;G:1904647649;T:2108525251;N:91361", 150, 150, null, null, 2143298124, 1896537115, 1904647649, 2108525251, 91361, "SRX9963415", "SRS8137082", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.94972, 0.94836, 0.0696, 0.0693, 0.75507, 0.75568, 0.48144, 0.48023, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63011, "SRR13565164", "SRX9963408", "SRS8137075", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep3", "GSM5047592", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 6pg ndr2 mRNA", "zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep3", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 6pg ndr2 mRNA", "GSM5047592", "GSM5047592: zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep3; Danio rerio; RNA Seq", "GSM5047592", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047592", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_30_6h_3_FRAS190081893-1a_1.clean.fq.gz wt_cyc_30_6h_3_FRAS190081893-1a_2.clean.fq.gz", "fastq fastq", 6204826800.0, 20682756.0, "GSM5047592 r1", "0:150 1:150", "A:1638571205;C:1478667441;G:1476954995;T:1610612834;N:20325", 150, 150, null, null, 1638571205, 1478667441, 1476954995, 1610612834, 20325, "SRX9963408", "SRS8137075", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95831, 0.95719, 0.0574, 0.05769, 0.76581, 0.76579, 0.47268, 0.47392, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63012, "SRR13565163", "SRX9963407", "SRS8137074", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep2", "GSM5047591", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 6pg ndr2 mRNA", "zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep2", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 6pg ndr2 mRNA", "GSM5047591", "GSM5047591: zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep2; Danio rerio; RNA Seq", "GSM5047591", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047591", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_30_6h_2_FRAS190081892-1a_1.clean.fq.gz wt_cyc_30_6h_2_FRAS190081892-1a_2.clean.fq.gz", "fastq fastq", 7831947600.0, 26106492.0, "GSM5047591 r1", "0:150 1:150", "A:2077699150;C:1855593864;G:1853962895;T:2044664440;N:27251", 150, 150, null, null, 2077699150, 1855593864, 1853962895, 2044664440, 27251, "SRX9963407", "SRS8137074", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95793, 0.95689, 0.0661, 0.06626, 0.76232, 0.76292, 0.48452, 0.48529, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63013, "SRR13565162", "SRX9963406", "SRS8137073", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep1", "GSM5047590", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 6pg ndr2 mRNA", "zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep1", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 6pg ndr2 mRNA", "GSM5047590", "GSM5047590: zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep1; Danio rerio; RNA Seq", "GSM5047590", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047590", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_30_6h_1_FRAS190081891-1a_1.clean.fq.gz wt_cyc_30_6h_1_FRAS190081891-1a_2.clean.fq.gz", "fastq fastq", 6204778800.0, 20682596.0, "GSM5047590 r1", "0:150 1:150", "A:1634567730;C:1482202802;G:1480166311;T:1607821234;N:20723", 150, 150, null, null, 1634567730, 1482202802, 1480166311, 1607821234, 20723, "SRX9963406", "SRS8137073", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95776, 0.95683, 0.05263, 0.0528, 0.76859, 0.76808, 0.46707, 0.46512, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63020, "SRR13565155", "SRX9963399", "SRS8137066", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep3", "GSM5047583", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 2pg ndr2 mRNA", "zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep3", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 2pg ndr2 mRNA", "GSM5047583", "GSM5047583: zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep3; Danio rerio; RNA Seq", "GSM5047583", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047583", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_10_6h_3_FRAS190081902-1a_1.clean.fq.gz wt_cyc_10_6h_3_FRAS190081902-1a_2.clean.fq.gz", "fastq fastq", 6854552700.0, 22848509.0, "GSM5047583 r1", "0:150 1:150", "A:1802480425;C:1637542682;G:1636679670;T:1777781400;N:68523", 150, 150, null, null, 1802480425, 1637542682, 1636679670, 1777781400, 68523, "SRX9963399", "SRS8137066", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.96086, 0.96074, 0.05567, 0.05502, 0.76374, 0.76386, 0.47217, 0.4745, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63021, "SRR13565154", "SRX9963398", "SRS8137065", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep2", "GSM5047582", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 2pg ndr2 mRNA", "zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep2", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 2pg ndr2 mRNA", "GSM5047582", "GSM5047582: zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep2; Danio rerio; RNA Seq", "GSM5047582", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047582", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_10_6h_2_FRAS190081901-1a_1.clean.fq.gz wt_cyc_10_6h_2_FRAS190081901-1a_2.clean.fq.gz", "fastq fastq", 6660902400.0, 22203008.0, "GSM5047582 r1", "0:150 1:150", "A:1752927278;C:1589205016;G:1589539254;T:1729165394;N:65458", 150, 150, null, null, 1752927278, 1589205016, 1589539254, 1729165394, 65458, "SRX9963398", "SRS8137065", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95957, 0.9592, 0.05754, 0.05704, 0.76861, 0.76901, 0.4689, 0.46677, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63022, "SRR13565153", "SRX9963397", "SRS8137064", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep1", "GSM5047581", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 2pg ndr2 mRNA", "zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep1", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 2pg ndr2 mRNA", "GSM5047581", "GSM5047581: zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep1; Danio rerio; RNA Seq", "GSM5047581", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047581", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_cyc_10_6h_1_FRAS190081900-1a_1.clean.fq.gz wt_cyc_10_6h_1_FRAS190081900-1a_2.clean.fq.gz", "fastq fastq", 6570978600.0, 21903262.0, "GSM5047581 r1", "0:150 1:150", "A:1741044737;C:1558378592;G:1557145638;T:1714386743;N:22890", 150, 150, null, null, 1741044737, 1558378592, 1557145638, 1714386743, 22890, "SRX9963397", "SRS8137064", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95798, 0.95712, 0.06166, 0.06223, 0.76512, 0.76727, 0.48467, 0.48609, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63029, "SRR13565146", "SRX9963390", "SRS8137058", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants control 6hpf rep3", "GSM5047574", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:control", "zebrafish explants control 6hpf rep3", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:control", "GSM5047574", "GSM5047574: zebrafish explants control 6hpf rep3; Danio rerio; RNA Seq", "GSM5047574", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047574", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_6h_3_FRAS190066751-1a_1.clean.fq.gz wt_6h_3_FRAS190066751-1a_2.clean.fq.gz", "fastq fastq", 8128685100.0, 27095617.0, "GSM5047574 r1", "0:150 1:150", "A:2156076550;C:1921161723;G:1927938071;T:2123415693;N:93063", 150, 150, null, null, 2156076550, 1921161723, 1927938071, 2123415693, 93063, "SRX9963390", "SRS8137058", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.9495, 0.94903, 0.07172, 0.07213, 0.75536, 0.7558, 0.48006, 0.47548, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63030, "SRR13565145", "SRX9963389", "SRS8137055", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants control 6hpf rep2", "GSM5047573", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:control", "zebrafish explants control 6hpf rep2", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:control", "GSM5047573", "GSM5047573: zebrafish explants control 6hpf rep2; Danio rerio; RNA Seq", "GSM5047573", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047573", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_6h_2_FRAS190066750-1a_1.clean.fq.gz wt_6h_2_FRAS190066750-1a_2.clean.fq.gz", "fastq fastq", 9247290000.0, 30824300.0, "GSM5047573 r1", "0:150 1:150", "A:2463506149;C:2176845523;G:2183719829;T:2423113642;N:104857", 150, 150, null, null, 2463506149, 2176845523, 2183719829, 2423113642, 104857, "SRX9963389", "SRS8137055", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.95086, 0.94915, 0.06721, 0.06691, 0.75497, 0.75657, 0.48339, 0.48399, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63031, "SRR13565144", "SRX9963388", "SRS8137056", "SRP303505", "PRJNA695273", "Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq]", "GSE165652", "Transcriptome Analysis", "Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish explants control 6hpf rep1", "GSM5047572", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:control", "zebrafish explants control 6hpf rep1", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene", "zebrafish cells", "10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50\u03bcg/\u03bcl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately.", "Total RNAs was extracted using TRIzol following the manufacturer\u2019s instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf|treatment:control", "GSM5047572", "GSM5047572: zebrafish explants control 6hpf rep1; Danio rerio; RNA Seq", "GSM5047572", null, "1", "Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5047572", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303505", null, null, "wt_6h_1_FRAS190066749-1a_1.clean.fq.gz wt_6h_1_FRAS190066749-1a_2.clean.fq.gz", "fastq fastq", 8383284300.0, 27944281.0, "GSM5047572 r1", "0:150 1:150", "A:2237361056;C:1969554479;G:1976393701;T:2199879679;N:95385", 150, 150, null, null, 2237361056, 1969554479, 1976393701, 2199879679, 95385, "SRX9963388", "SRS8137056", "SRA1188620", "GEO", "Institute of genetics, Zhejiang University", 2, 0.94782, 0.94694, 0.07354, 0.07393, 0.75471, 0.7555, 0.47481, 0.47344, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [65748, "SRR15600933", "SRX11898446", "SRS9909628", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Adar OE 5.3hpf rep2", "GSM5535062", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Adar OE 5.3hpf rep2", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535062", "GSM5535062: Adar OE 5.3hpf rep2; Danio rerio; RNA Seq", "GSM5535062", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535062", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "P4_mRNA_50perc_ep_R1.fastq.gz P4_mRNA_50perc_ep_R2.fastq.gz", "fastq fastq", 1326845632.0, 5119690.0, "GSM5535062 r1", "0:127.74 1:131.43", "A:352357573;C:311209382;G:333436270;T:329477541;N:364866", 127, 131, null, null, 352357573, 311209382, 333436270, 329477541, 364866, "SRX11898446", "SRS9909628", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.82821, 0.82088, 0.13688, 0.13203, 0.78709, 0.81582, 0.50433, 0.50688, 149, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65749, "SRR15600932", "SRX11898445", "SRS9909627", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Adar OE 5.3hpf rep1", "GSM5535061", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Adar OE 5.3hpf rep1", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535061", "GSM5535061: Adar OE 5.3hpf rep1; Danio rerio; RNA Seq", "GSM5535061", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "P1_mRNA_50perc_ep_R1.fastq.gz P1_mRNA_50perc_ep_R2.fastq.gz", "fastq fastq", 1938618402.0, 7874419.0, "GSM5535061 r1", "0:120.22 1:125.97", "A:505667508;C:461531998;G:503358589;T:467210132;N:850175", 120, 125, null, null, 505667508, 461531998, 503358589, 467210132, 850175, "SRX11898445", "SRS9909627", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.82249, 0.81278, 0.13915, 0.13457, 0.77398, 0.80756, 0.5303, 0.53027, 61, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65752, "SRR23490199", "SRX11898442", "SRS9909624", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Adar MO 5.3hpf rep 2", "GSM5535058", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Adar MO 5.3hpf rep 2", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535058", "GSM5535058: Adar MO 5.3hpf rep 2; Danio rerio; RNA Seq", "GSM5535058", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535058", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "P4_MO_50perc_ep_R1.fastq.gz P4_MO_50perc_ep_R2.fastq.gz", "fastq fastq", 4610706851.0, 32131419.0, "GSM5535058 r11", "0:71.55 1:71.95", "A:1154252900;C:1100883544;G:1174376934;T:1177509806;N:3683667", 71, 71, null, null, 1154252900, 1100883544, 1174376934, 1177509806, 3683667, "SRX11898442", "SRS9909624", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.83762, 0.86455, 0.18676, 0.17496, 0.7332, 0.74961, 0.50535, 0.49929, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65753, "SRR23490182", "SRX11898441", "SRS9909623", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Adar MO 5.3hpf rep 1", "GSM5535057", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Adar MO 5.3hpf rep 1", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535057", "GSM5535057: Adar MO 5.3hpf rep 1; Danio rerio; RNA Seq", "GSM5535057", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "P1_MO_50perc_ep_R1.fastq.gz P1_MO_50perc_ep_R2.fastq.gz", "fastq fastq", 3449084411.0, 24590980.0, "GSM5535057 r11", "0:69.91 1:70.34", "A:851251460;C:838832857;G:894260069;T:859903103;N:4836922", 69, 70, null, null, 851251460, 838832857, 894260069, 859903103, 4836922, "SRX11898441", "SRS9909623", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.82688, 0.84314, 0.20737, 0.19391, 0.72685, 0.73708, 0.50595, 0.4979, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65756, "SRR23490198", "SRX11898438", "SRS9909620", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Control 5.3hpf rep 2", "GSM5535052", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Control 5.3hpf rep 2", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535052", "GSM5535052: Control 5.3hpf rep 2; Danio rerio; RNA Seq", "GSM5535052", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "P4_CTR_50perc_ep_R1.fastq.gz P4_CTR_50perc_ep_R2.fastq.gz", "fastq fastq", 2923737162.0, 21542650.0, "GSM5535052 r11", "0:67.56 1:68.16", "A:721223774;C:711238075;G:755345990;T:731167792;N:4761531", 67, 68, null, null, 721223774, 711238075, 755345990, 731167792, 4761531, "SRX11898438", "SRS9909620", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.78649, 0.80254, 0.15793, 0.14741, 0.73766, 0.74888, 0.50253, 0.50701, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65757, "SRR15600924", "SRX11898437", "SRS9909619", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Control 5.3hpf rep 1", "GSM5535051", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Control 5.3hpf rep 1", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535051", "GSM5535051: Control 5.3hpf rep 1; Danio rerio; RNA Seq", "GSM5535051", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "P1_CTR_50perc_ep_R1.fastq.gz P1_CTR_50perc_ep_R2.fastq.gz", "fastq fastq", 1880591854.0, 7796990.0, "GSM5535051 r1", "0:117.90 1:123.29", "A:483040278;C:455828987;G:494055390;T:446579011;N:1088188", 117, 123, null, null, 483040278, 455828987, 494055390, 446579011, 1088188, "SRX11898437", "SRS9909619", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.81244, 0.79845, 0.16732, 0.16048, 0.78464, 0.813, 0.52582, 0.53356, 132, 132, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65760, "SRR15600918", "SRX11898434", "SRS9909616", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Offspring 5.3hpf", "GSM5535047", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Offspring 5.3hpf", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535047", "GSM5535047: Offspring 5.3hpf; Danio rerio; RNA Seq", "GSM5535047", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "4-5-3h_S2_L001_R1_001.fastq.gz 4-5-3h_S2_L001_R2_001.fastq.gz", "fastq fastq", 1921971826.0, 12727220.0, "GSM5535047 r1", "0:75.51 1:75.50", "A:517361178;C:458139401;G:447412846;T:498487503;N:570898", 75, 75, null, null, 517361178, 458139401, 447412846, 498487503, 570898, "SRX11898434", "SRS9909616", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92273, 0.92291, 0.19118, 0.19336, 0.73123, 0.7361, 0.47818, 0.47715, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65761, "SRR15600919", "SRX11898434", "SRS9909616", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Offspring 5.3hpf", "GSM5535047", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Offspring 5.3hpf", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535047", "GSM5535047: Offspring 5.3hpf; Danio rerio; RNA Seq", "GSM5535047", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "4-5-3h_S2_L002_R1_001.fastq.gz 4-5-3h_S2_L002_R2_001.fastq.gz", "fastq fastq", 1917366096.0, 12696801.0, "GSM5535047 r2", "0:75.51 1:75.50", "A:517114724;C:456831675;G:445832667;T:497081776;N:505254", 75, 75, null, null, 517114724, 456831675, 445832667, 497081776, 505254, "SRX11898434", "SRS9909616", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92312, 0.92315, 0.19106, 0.19223, 0.73032, 0.73606, 0.48162, 0.4828, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65762, "SRR15600920", "SRX11898434", "SRS9909616", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Offspring 5.3hpf", "GSM5535047", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Offspring 5.3hpf", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535047", "GSM5535047: Offspring 5.3hpf; Danio rerio; RNA Seq", "GSM5535047", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "4-5-3h_S2_L003_R1_001.fastq.gz 4-5-3h_S2_L003_R2_001.fastq.gz", "fastq fastq", 1775847487.0, 11759781.0, "GSM5535047 r3", "0:75.51 1:75.50", "A:481069889;C:421508961;G:412411876;T:460605903;N:250858", 75, 75, null, null, 481069889, 421508961, 412411876, 460605903, 250858, "SRX11898434", "SRS9909616", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.9196, 0.92129, 0.19154, 0.19449, 0.73507, 0.7415, 0.47795, 0.4769, 76, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [65763, "SRR15600921", "SRX11898434", "SRS9909616", "SRP333957", "PRJNA757460", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish", "GSE182714", "Other", "Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 \u00d7 75 bp reads was performed with NextSeq 500 Illumina USA.", null, "pubmed:36127363", null, "Offspring 5.3hpf", "GSM5535047", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "Offspring 5.3hpf", "Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10\u00a0 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10\u00a0 Supplementary files format and content: tab delimited file format", "whole zebrafish embryo", "To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina USA.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.", "strain:WT ABTL|tissue:whole embryo|developmental stage:5.3hpf", "GSM5535047", "GSM5535047: Offspring 5.3hpf; Danio rerio; RNA Seq", "GSM5535047", null, "1", "Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.", "GEO Accession:GSM5535047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "4-5-3h_S2_L004_R1_001.fastq.gz 4-5-3h_S2_L004_R2_001.fastq.gz", "fastq fastq", 1797045896.0, 11900141.0, "GSM5535047 r4", "0:75.51 1:75.50", "A:487552361;C:426340837;G:416701776;T:466214869;N:236053", 75, 75, null, null, 487552361, 426340837, 416701776, 466214869, 236053, "SRX11898434", "SRS9909616", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.91846, 0.92025, 0.19213, 0.19409, 0.73553, 0.7429, 0.47854, 0.4801, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [70026, "SRR19364711", "SRX15423222", "SRS13146638", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cm.Bf.10hpf 4 RNA seq", "GSM6180954", null, "source name:Cm.Bf.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "Cm.Bf.10hpf 4 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cm.Bf.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "GSM6180954", "GSM6180954: Cm.Bf.10hpf 4 RNA seq; Danio rerio; RNA Seq", "GSM6180954 r1", "GSM6180954", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CmBf_10_hpf_16_R1.fastq.gz CmBf_10_hpf_16_R2.fastq.gz", "fastq fastq", 17113906800.0, 57046356.0, "GSM6180954 r1", "0:150 1:150", "A:4335140159;C:4129743628;G:4430801624;T:4217263474;N:957915", 150, 150, null, null, 4335140159, 4129743628, 4430801624, 4217263474, 957915, "SRX15423222", "SRS13146638", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94211, 0.92928, 0.16107, 0.15738, 0.76337, 0.76499, 0.60714, 0.61164, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70027, "SRR19364712", "SRX15423221", "SRS13146637", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cm.Bf.10hpf 3 RNA seq", "GSM6180953", null, "source name:Cm.Bf.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "Cm.Bf.10hpf 3 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cm.Bf.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "GSM6180953", "GSM6180953: Cm.Bf.10hpf 3 RNA seq; Danio rerio; RNA Seq", "GSM6180953 r1", "GSM6180953", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CmBf_10_hpf_15_R1.fastq.gz CmBf_10_hpf_15_R2.fastq.gz", "fastq fastq", 19206853500.0, 64022845.0, "GSM6180953 r1", "0:150 1:150", "A:4980230724;C:4537728686;G:4835230280;T:4852563612;N:1100198", 150, 150, null, null, 4980230724, 4537728686, 4835230280, 4852563612, 1100198, "SRX15423221", "SRS13146637", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93741, 0.92352, 0.14599, 0.13986, 0.76394, 0.76603, 0.60186, 0.60565, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70028, "SRR19364713", "SRX15423220", "SRS13146636", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cm.Bf.10hpf 2 RNA seq", "GSM6180952", null, "source name:Cm.Bf.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "Cm.Bf.10hpf 2 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cm.Bf.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "GSM6180952", "GSM6180952: Cm.Bf.10hpf 2 RNA seq; Danio rerio; RNA Seq", "GSM6180952 r1", "GSM6180952", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CmBf_10_hpf_14_R1.fastq.gz CmBf_10_hpf_14_R2.fastq.gz", "fastq fastq", 17479590000.0, 58265300.0, "GSM6180952 r1", "0:150 1:150", "A:4443574382;C:4199857708;G:4510495634;T:4324667842;N:994434", 150, 150, null, null, 4443574382, 4199857708, 4510495634, 4324667842, 994434, "SRX15423220", "SRS13146636", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94666, 0.93479, 0.15687, 0.15334, 0.7626, 0.76439, 0.61598, 0.61821, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70029, "SRR19364714", "SRX15423219", "SRS13146635", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cm.Bf.10hpf 1 RNA seq", "GSM6180951", null, "source name:Cm.Bf.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "Cm.Bf.10hpf 1 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cm.Bf.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control male x BaP female", "GSM6180951", "GSM6180951: Cm.Bf.10hpf 1 RNA seq; Danio rerio; RNA Seq", "GSM6180951 r1", "GSM6180951", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CmBf_10_hpf_13_R1.fastq.gz CmBf_10_hpf_13_R2.fastq.gz", "fastq fastq", 19990365900.0, 66634553.0, "GSM6180951 r1", "0:150 1:150", "A:5155741561;C:4767612131;G:5049305152;T:5016573262;N:1133794", 150, 150, null, null, 5155741561, 4767612131, 5049305152, 5016573262, 1133794, "SRX15423219", "SRS13146635", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93836, 0.92507, 0.15559, 0.15141, 0.7573, 0.75808, 0.49581, 0.60633, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70030, "SRR19364715", "SRX15423218", "SRS13146634", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cf.Bm.10hpf 4 RNA seq", "GSM6180950", null, "source name:Cf.Bm.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "Cf.Bm.10hpf 4 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cf.Bm.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "GSM6180950", "GSM6180950: Cf.Bm.10hpf 4 RNA seq; Danio rerio; RNA Seq", "GSM6180950 r1", "GSM6180950", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CfBm_10_hpf_20_R1.fastq.gz CfBm_10_hpf_20_R2.fastq.gz", "fastq fastq", 21211295100.0, 70704317.0, "GSM6180950 r1", "0:150 1:150", "A:5311122548;C:5167766822;G:5550521302;T:5180671668;N:1212760", 150, 150, null, null, 5311122548, 5167766822, 5550521302, 5180671668, 1212760, "SRX15423218", "SRS13146634", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93439, 0.92762, 0.15353, 0.15251, 0.77135, 0.77319, 0.52474, 0.59471, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70031, "SRR19364716", "SRX15423217", "SRS13146633", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cf.Bm.10hpf 3 RNA seq", "GSM6180949", null, "source name:Cf.Bm.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "Cf.Bm.10hpf 3 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cf.Bm.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "GSM6180949", "GSM6180949: Cf.Bm.10hpf 3 RNA seq; Danio rerio; RNA Seq", "GSM6180949 r1", "GSM6180949", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CfBm_10_hpf_19_R1.fastq.gz CfBm_10_hpf_19_R2.fastq.gz", "fastq fastq", 15181185900.0, 50603953.0, "GSM6180949 r1", "0:150 1:150", "A:3861473177;C:3660503174;G:3897945836;T:3760408062;N:855651", 150, 150, null, null, 3861473177, 3660503174, 3897945836, 3760408062, 855651, "SRX15423217", "SRS13146633", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94566, 0.93343, 0.15293, 0.14934, 0.76564, 0.7667, 0.60808, 0.6141, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70032, "SRR19364717", "SRX15423216", "SRS13146632", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cf.Bm.10hpf 2 RNA seq", "GSM6180948", null, "source name:Cf.Bm.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "Cf.Bm.10hpf 2 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cf.Bm.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "GSM6180948", "GSM6180948: Cf.Bm.10hpf 2 RNA seq; Danio rerio; RNA Seq", "GSM6180948 r1", "GSM6180948", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CfBm_10_hpf_18_R1.fastq.gz CfBm_10_hpf_18_R2.fastq.gz", "fastq fastq", 19820526900.0, 66068423.0, "GSM6180948 r1", "0:150 1:150", "A:4972408439;C:4835381551;G:5174213471;T:4837395455;N:1127984", 150, 150, null, null, 4972408439, 4835381551, 5174213471, 4837395455, 1127984, "SRX15423216", "SRS13146632", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.95061, 0.93663, 0.1414, 0.13768, 0.7696, 0.77264, 0.62446, 0.62332, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70033, "SRR19364718", "SRX15423215", "SRS13146631", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "Cf.Bm.10hpf 1 RNA seq", "GSM6180947", null, "source name:Cf.Bm.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "Cf.Bm.10hpf 1 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "Cf.Bm.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "GSM6180947", "GSM6180947: Cf.Bm.10hpf 1 RNA seq; Danio rerio; RNA Seq", "GSM6180947 r1", "GSM6180947", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP376709", null, "loader:fastq load.py", "CfBm_10_hpf_17_R1.fastq.gz CfBm_10_hpf_17_R2.fastq.gz", "fastq fastq", 18690339000.0, 62301130.0, "GSM6180947 r1", "0:150 1:150", "A:4803588863;C:4456713432;G:4745443898;T:4683543334;N:1049473", 150, 150, null, null, 4803588863, 4456713432, 4745443898, 4683543334, 1049473, "SRX15423215", "SRS13146631", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93704, 0.92097, 0.12864, 0.1241, 0.76879, 0.77059, 0.61593, 0.61609, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", 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