{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and technology = \"bulk\"", "rows": [[30028, "SRR27732024", "SRX23397624", "SRS20258465", "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 12 hpf embryo", "zebrafish embryo 12hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 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: 12hpf embryo", "W 9", "W 9", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT12h-3_1.fq.gz WT12h-3_2.fq.gz", "fastq fastq", 6455561100.0, 21518537.0, "WT12h 3 1.fq.gz", "0:150 1:150", "A:1703515693;C:1511743995;G:1560331864;T:1679864521;N:105027", 150, 150, null, null, 1703515693, 1511743995, 1560331864, 1679864521, 105027, "SRX23397624", "SRS20258465", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94111, 0.94086, 0.06759, 0.06714, 0.74383, 0.74479, 0.46264, 0.46309, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30029, "SRR27732025", "SRX23397623", "SRS20258464", "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 12 hpf embryo", "zebrafish embryo 12hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 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: 12hpf embryo", "W 8", "W 8", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT12h-2_1.fq.gz WT12h-2_2.fq.gz", "fastq fastq", 6161839200.0, 20539464.0, "WT12h 2 1.fq.gz", "0:150 1:150", "A:1628002733;C:1440787634;G:1486546983;T:1606403484;N:98366", 150, 150, null, null, 1628002733, 1440787634, 1486546983, 1606403484, 98366, "SRX23397623", "SRS20258464", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94064, 0.93857, 0.06897, 0.06866, 0.7457, 0.74621, 0.46575, 0.46211, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30030, "SRR27732026", "SRX23397622", "SRS20258463", "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 12 hpf embryo", "zebrafish embryo 12hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 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: 12hpf embryo", "W 7", "W 7", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT12h-1_2.fq.gz WT12h-1_1.fq.gz", "fastq fastq", 6395259000.0, 21317530.0, "WT12h 1 1.fq.gz", "0:150 1:150", "A:1700786034;C:1487669685;G:1530455534;T:1676243983;N:103764", 150, 150, null, null, 1700786034, 1487669685, 1530455534, 1676243983, 103764, "SRX23397622", "SRS20258463", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94192, 0.9393, 0.07278, 0.0714, 0.74225, 0.74414, 0.46258, 0.46623, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30043, "SRR27730706", "SRX23396352", "SRS20257266", "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 /  12 hpf embryo", "zebrafish embryo hamp /  12hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 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: 12hpf embryo", "W 30", "W 30", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp12h-3_1.fq.gz hamp12h-3_2.fq.gz", "fastq fastq", 6380262000.0, 21267540.0, "hamp12h 3 1.fq.gz", "0:150 1:150", "A:1686482981;C:1496556670;G:1525661866;T:1671347887;N:212596", 150, 150, null, null, 1686482981, 1496556670, 1525661866, 1671347887, 212596, "SRX23396352", "SRS20257266", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93955, 0.93782, 0.07021, 0.07017, 0.72541, 0.72691, 0.4754, 0.47596, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30044, "SRR27730707", "SRX23396351", "SRS20257265", "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 /  12 hpf embryo", "zebrafish embryo hamp /  12hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 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: 12hpf embryo", "W 29", "W 29", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp12h-2_1.fq.gz hamp12h-2_2.fq.gz", "fastq fastq", 6738373500.0, 22461245.0, "hamp12h 2 1.fq.gz", "0:150 1:150", "A:1793407846;C:1570428903;G:1600911780;T:1773421988;N:202983", 150, 150, null, null, 1793407846, 1570428903, 1600911780, 1773421988, 202983, "SRX23396351", "SRS20257265", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93629, 0.93637, 0.07013, 0.07043, 0.72764, 0.72912, 0.47138, 0.47279, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30045, "SRR27730708", "SRX23396350", "SRS20257264", "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 /  12 hpf embryo", "zebrafish embryo hamp /  12hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 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: 12hpf embryo", "W 28", "W 28", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp12h-1_1.fq.gz hamp12h-1_2.fq.gz", "fastq fastq", 6882364200.0, 22941214.0, "hamp12h 1 1.fq.gz", "0:150 1:150", "A:1816338301;C:1617411981;G:1650700092;T:1797708715;N:205111", 150, 150, null, null, 1816338301, 1617411981, 1650700092, 1797708715, 205111, "SRX23396350", "SRS20257264", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93465, 0.93675, 0.06811, 0.06816, 0.72863, 0.72922, 0.47838, 0.47563, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31557, "SRR28471021", "SRX24074012", "SRS20864401", "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, "S16 slice 13", "GSM8171995", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171995", "GSM8171995: S16 slice 13; Danio rerio; RNA Seq", "GSM8171995 r1", "GSM8171995", "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", "S16_2_13-R1.fq.gz S16_2_13-R2.fq.gz", "fastq fastq", 7021136766.0, 24220886.0, "GSM8171995 r1", "0:143.40 1:146.48", "A:1932409729;C:1613003140;G:1510879854;T:1964782006;N:62037", 143, 146, null, null, 1932409729, 1613003140, 1510879854, 1964782006, 62037, "SRX24074012", "SRS20864401", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31558, "SRR28471022", "SRX24074011", "SRS20864400", "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, "S16 slice 12", "GSM8171993", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171993", "GSM8171993: S16 slice 12; Danio rerio; RNA Seq", "GSM8171993 r1", "GSM8171993", "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", "S16_2_12-R1.fq.gz S16_2_12-R2.fq.gz", "fastq fastq", 6989496704.0, 24013496.0, "GSM8171993 r1", "0:144.73 1:146.34", "A:1973063613;C:1539634004;G:1502105630;T:1974633280;N:60177", 144, 146, null, null, 1973063613, 1539634004, 1502105630, 1974633280, 60177, "SRX24074011", "SRS20864400", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31559, "SRR28471023", "SRX24074010", "SRS20864399", "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, "S16 slice 11", "GSM8171992", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171992", "GSM8171992: S16 slice 11; Danio rerio; RNA Seq", "GSM8171992 r1", "GSM8171992", "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", "S16_2_11-R1.fq.gz S16_2_11-R2.fq.gz", "fastq fastq", 6658580843.0, 22968779.0, "GSM8171992 r1", "0:143.28 1:146.62", "A:1850547171;C:1505778383;G:1450300777;T:1851895401;N:59111", 143, 146, null, null, 1850547171, 1505778383, 1450300777, 1851895401, 59111, "SRX24074010", "SRS20864399", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31560, "SRR28471024", "SRX24074009", "SRS20864398", "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, "S16 slice 10", "GSM8171991", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171991", "GSM8171991: S16 slice 10; Danio rerio; RNA Seq", "GSM8171991 r1", "GSM8171991", "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", "S16_2_10-R1.fq.gz S16_2_10-R2.fq.gz", "fastq fastq", 6764254234.0, 23283773.0, "GSM8171991 r1", "0:143.52 1:146.99", "A:1876570759;C:1531892471;G:1478929048;T:1876804139;N:57817", 143, 146, null, null, 1876570759, 1531892471, 1478929048, 1876804139, 57817, "SRX24074009", "SRS20864398", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31561, "SRR28471025", "SRX24074008", "SRS20864397", "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, "S16 slice 9", "GSM8171990", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171990", "GSM8171990: S16 slice 9; Danio rerio; RNA Seq", "GSM8171990 r1", "GSM8171990", "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", "S16_2_09-R1.fq.gz S16_2_09-R2.fq.gz", "fastq fastq", 6953469676.0, 23939332.0, "GSM8171990 r1", "0:143.01 1:147.45", "A:1887466615;C:1613826863;G:1550286679;T:1901843452;N:46067", 143, 147, null, null, 1887466615, 1613826863, 1550286679, 1901843452, 46067, "SRX24074008", "SRS20864397", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31562, "SRR28471026", "SRX24074007", "SRS20864396", "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, "S16 slice 8", "GSM8171989", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171989", "GSM8171989: S16 slice 8; Danio rerio; RNA Seq", "GSM8171989 r1", "GSM8171989", "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", "S16_2_08-R1.fq.gz S16_2_08-R2.fq.gz", "fastq fastq", 6932164944.0, 23736001.0, "GSM8171989 r1", "0:144.93 1:147.12", "A:1878823532;C:1592513147;G:1541045989;T:1919723182;N:59094", 144, 147, null, null, 1878823532, 1592513147, 1541045989, 1919723182, 59094, "SRX24074007", "SRS20864396", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31563, "SRR28471027", "SRX24074006", "SRS20864395", "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, "S16 slice 7", "GSM8171987", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171987", "GSM8171987: S16 slice 7; Danio rerio; RNA Seq", "GSM8171987 r1", "GSM8171987", "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", "S16_2_07-R1.fq.gz S16_2_07-R2.fq.gz", "fastq fastq", 7175124342.0, 24613098.0, "GSM8171987 r1", "0:144.89 1:146.63", "A:1955179901;C:1642901455;G:1556429416;T:2020550025;N:63545", 144, 146, null, null, 1955179901, 1642901455, 1556429416, 2020550025, 63545, "SRX24074006", "SRS20864395", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31564, "SRR28471028", "SRX24074005", "SRS20864394", "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, "S16 slice 6", "GSM8171986", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171986", "GSM8171986: S16 slice 6; Danio rerio; RNA Seq", "GSM8171986 r1", "GSM8171986", "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", "S16_2_06-R1.fq.gz S16_2_06-R2.fq.gz", "fastq fastq", 7015063214.0, 24014594.0, "GSM8171986 r1", "0:145.26 1:146.86", "A:1907017747;C:1603933957;G:1551829473;T:1952222046;N:59991", 145, 146, null, null, 1907017747, 1603933957, 1551829473, 1952222046, 59991, "SRX24074005", "SRS20864394", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31565, "SRR28471029", "SRX24074004", "SRS20864393", "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, "S16 slice 5", "GSM8171985", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171985", "GSM8171985: S16 slice 5; Danio rerio; RNA Seq", "GSM8171985 r1", "GSM8171985", "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", "S16_2_05-R1.fq.gz S16_2_05-R2.fq.gz", "fastq fastq", 6919538718.0, 23740085.0, "GSM8171985 r1", "0:144.96 1:146.51", "A:1882346373;C:1593041314;G:1504597309;T:1939492468;N:61254", 144, 146, null, null, 1882346373, 1593041314, 1504597309, 1939492468, 61254, "SRX24074004", "SRS20864393", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31566, "SRR28471030", "SRX24074003", "SRS20864392", "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, "S16 slice 4", "GSM8171984", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171984", "GSM8171984: S16 slice 4; Danio rerio; RNA Seq", "GSM8171984 r1", "GSM8171984", "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", "S16_2_04-R1.fq.gz S16_2_04-R2.fq.gz", "fastq fastq", 6868276226.0, 23671591.0, "GSM8171984 r1", "0:144.21 1:145.94", "A:1877392790;C:1565333202;G:1481973920;T:1943515595;N:60719", 144, 145, null, null, 1877392790, 1565333202, 1481973920, 1943515595, 60719, "SRX24074003", "SRS20864392", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31567, "SRR28471031", "SRX24074002", "SRS20864391", "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, "S16 slice 3", "GSM8171983", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171983", "GSM8171983: S16 slice 3; Danio rerio; RNA Seq", "GSM8171983 r1", "GSM8171983", "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", "S16_2_03-R1.fq.gz S16_2_03-R2.fq.gz", "fastq fastq", 6805653527.0, 23393184.0, "GSM8171983 r1", "0:144.38 1:146.54", "A:1865258599;C:1547577456;G:1497746987;T:1895011008;N:59477", 144, 146, null, null, 1865258599, 1547577456, 1497746987, 1895011008, 59477, "SRX24074002", "SRS20864391", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31568, "SRR28471032", "SRX24074001", "SRS20864390", "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, "S16 slice 2", "GSM8171981", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171981", "GSM8171981: S16 slice 2; Danio rerio; RNA Seq", "GSM8171981 r1", "GSM8171981", "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", "S16_2_02-R1.fq.gz S16_2_02-R2.fq.gz", "fastq fastq", 7023963229.0, 24162141.0, "GSM8171981 r1", "0:144.12 1:146.58", "A:1918527133;C:1603910134;G:1551695853;T:1949772309;N:57800", 144, 146, null, null, 1918527133, 1603910134, 1551695853, 1949772309, 57800, "SRX24074001", "SRS20864390", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31569, "SRR28471033", "SRX24074000", "SRS20864389", "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, "S16 slice 1", "GSM8171980", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 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:16 hpf", "GSM8171980", "GSM8171980: S16 slice 1; Danio rerio; RNA Seq", "GSM8171980 r1", "GSM8171980", "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", "S16_2_01-R1.fq.gz S16_2_01-R2.fq.gz", "fastq fastq", 6619993068.0, 22789527.0, "GSM8171980 r1", "0:143.43 1:147.06", "A:1776228931;C:1542516186;G:1481044120;T:1820158687;N:45144", 143, 147, null, null, 1776228931, 1542516186, 1481044120, 1820158687, 45144, "SRX24074000", "SRS20864389", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31570, "SRR28471034", "SRX24073999", "SRS20864388", "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, "S12 slice 12", "GSM8171979", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171979", "GSM8171979: S12 slice 12; Danio rerio; RNA Seq", "GSM8171979 r1", "GSM8171979", "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", "S12_1_12-R1.fq.gz S12_1_12-R2.fq.gz", "fastq fastq", 6907282671.0, 23557012.0, "GSM8171979 r1", "0:145.54 1:147.68", "A:1862944199;C:1601198280;G:1521830219;T:1921292527;N:17446", 145, 147, null, null, 1862944199, 1601198280, 1521830219, 1921292527, 17446, "SRX24073999", "SRS20864388", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31571, "SRR28471035", "SRX24073998", "SRS20864387", "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, "S12 slice 11", "GSM8171978", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171978", "GSM8171978: S12 slice 11; Danio rerio; RNA Seq", "GSM8171978 r1", "GSM8171978", "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", "S12_1_11-R1.fq.gz S12_1_11-R2.fq.gz", "fastq fastq", 6831871099.0, 23334246.0, "GSM8171978 r1", "0:145.23 1:147.56", "A:1841130963;C:1590884839;G:1490156717;T:1909681306;N:17274", 145, 147, null, null, 1841130963, 1590884839, 1490156717, 1909681306, 17274, "SRX24073998", "SRS20864387", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31572, "SRR28471036", "SRX24073997", "SRS20864386", "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, "S12 slice 10", "GSM8171977", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171977", "GSM8171977: S12 slice 10; Danio rerio; RNA Seq", "GSM8171977 r1", "GSM8171977", "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", "S12_1_10-R1.fq.gz S12_1_10-R2.fq.gz", "fastq fastq", 5783041643.0, 19665431.0, "GSM8171977 r1", "0:146.19 1:147.88", "A:1581046379;C:1324978876;G:1248026718;T:1628974699;N:14971", 146, 147, null, null, 1581046379, 1324978876, 1248026718, 1628974699, 14971, "SRX24073997", "SRS20864386", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31573, "SRR28471037", "SRX24073996", "SRS20864385", "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, "S12 slice 9", "GSM8171976", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171976", "GSM8171976: S12 slice 9; Danio rerio; RNA Seq", "GSM8171976 r1", "GSM8171976", "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", "S12_1_09-R1.fq.gz S12_1_09-R2.fq.gz", "fastq fastq", 7123142895.0, 24299296.0, "GSM8171976 r1", "0:145.49 1:147.66", "A:1925297375;C:1659640314;G:1576196761;T:1961990580;N:17865", 145, 147, null, null, 1925297375, 1659640314, 1576196761, 1961990580, 17865, "SRX24073996", "SRS20864385", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31574, "SRR28471038", "SRX24073995", "SRS20864384", "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, "S12 slice 8", "GSM8171974", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171974", "GSM8171974: S12 slice 8; Danio rerio; RNA Seq", "GSM8171974 r1", "GSM8171974", "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", "S12_1_08-R1.fq.gz S12_1_08-R2.fq.gz", "fastq fastq", 7144819692.0, 24316501.0, "GSM8171974 r1", "0:145.93 1:147.90", "A:1915884877;C:1672968137;G:1576641332;T:1979307110;N:18236", 145, 147, null, null, 1915884877, 1672968137, 1576641332, 1979307110, 18236, "SRX24073995", "SRS20864384", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31575, "SRR28471039", "SRX24073994", "SRS20864383", "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, "S12 slice 7", "GSM8171973", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171973", "GSM8171973: S12 slice 7; Danio rerio; RNA Seq", "GSM8171973 r1", "GSM8171973", "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", "S12_1_07-R1.fq.gz S12_1_07-R2.fq.gz", "fastq fastq", 7379485401.0, 25300209.0, "GSM8171973 r1", "0:143.87 1:147.81", "A:1973584695;C:1736374415;G:1654430758;T:2015077010;N:18523", 143, 147, null, null, 1973584695, 1736374415, 1654430758, 2015077010, 18523, "SRX24073994", "SRS20864383", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31576, "SRR28471040", "SRX24073993", "SRS20864382", "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, "S12 slice 6", "GSM8171972", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171972", "GSM8171972: S12 slice 6; Danio rerio; RNA Seq", "GSM8171972 r1", "GSM8171972", "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", "S12_1_06-R1.fq.gz S12_1_06-R2.fq.gz", "fastq fastq", 6780830499.0, 23111786.0, "GSM8171972 r1", "0:145.59 1:147.80", "A:1809593504;C:1599719267;G:1512122288;T:1859381851;N:13589", 145, 147, null, null, 1809593504, 1599719267, 1512122288, 1859381851, 13589, "SRX24073993", "SRS20864382", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31577, "SRR28471041", "SRX24073992", "SRS20864381", "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, "S12 slice 5", "GSM8171971", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171971", "GSM8171971: S12 slice 5; Danio rerio; RNA Seq", "GSM8171971 r1", "GSM8171971", "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", "S12_1_05-R1.fq.gz S12_1_05-R2.fq.gz", "fastq fastq", 6959350050.0, 23769190.0, "GSM8171971 r1", "0:145.06 1:147.72", "A:1875092128;C:1615063748;G:1550970555;T:1918160024;N:63595", 145, 147, null, null, 1875092128, 1615063748, 1550970555, 1918160024, 63595, "SRX24073992", "SRS20864381", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31578, "SRR28471042", "SRX24073991", "SRS20864380", "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, "S12 slice 4", "GSM8171970", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171970", "GSM8171970: S12 slice 4; Danio rerio; RNA Seq", "GSM8171970 r1", "GSM8171970", "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", "S12_1_04-R1.fq.gz S12_1_04-R2.fq.gz", "fastq fastq", 7016331930.0, 23929575.0, "GSM8171970 r1", "0:145.36 1:147.85", "A:1883672645;C:1639902329;G:1566256062;T:1926486960;N:13934", 145, 147, null, null, 1883672645, 1639902329, 1566256062, 1926486960, 13934, "SRX24073991", "SRS20864380", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31579, "SRR28471043", "SRX24073990", "SRS20864379", "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, "S12 slice 3", "GSM8171968", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171968", "GSM8171968: S12 slice 3; Danio rerio; RNA Seq", "GSM8171968 r1", "GSM8171968", "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", "S12_1_03-R1.fq.gz S12_1_03-R2.fq.gz", "fastq fastq", 7014757897.0, 23928375.0, "GSM8171968 r1", "0:145.38 1:147.78", "A:1893627672;C:1629188725;G:1555319202;T:1936558222;N:64076", 145, 147, null, null, 1893627672, 1629188725, 1555319202, 1936558222, 64076, "SRX24073990", "SRS20864379", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31580, "SRR28471044", "SRX24073989", "SRS20864378", "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, "S12 slice 2", "GSM8171967", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171967", "GSM8171967: S12 slice 2; Danio rerio; RNA Seq", "GSM8171967 r1", "GSM8171967", "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", "S12_1_02-R1.fq.gz S12_1_02-R2.fq.gz", "fastq fastq", 6840908671.0, 23398529.0, "GSM8171967 r1", "0:144.87 1:147.50", "A:1887167845;C:1555902053;G:1495740904;T:1902033708;N:64161", 144, 147, null, null, 1887167845, 1555902053, 1495740904, 1902033708, 64161, "SRX24073989", "SRS20864378", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31581, "SRR28471045", "SRX24073988", "SRS20864376", "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, "S12 slice 1", "GSM8171966", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 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:12 hpf", "GSM8171966", "GSM8171966: S12 slice 1; Danio rerio; RNA Seq", "GSM8171966 r1", "GSM8171966", "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", "S12_1_01-R1.fq.gz S12_1_01-R2.fq.gz", "fastq fastq", 7278647579.0, 24915967.0, "GSM8171966 r1", "0:144.68 1:147.45", "A:1978225177;C:1677337831;G:1598910902;T:2024108056;N:65613", 144, 147, null, null, 1978225177, 1677337831, 1598910902, 2024108056, 65613, "SRX24073988", "SRS20864376", "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", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37221, "SRR1035984", "SRX381838", "SRS506055", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "Wild type AB strain rep1", "GSM1273590", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type AB strain", "Wild type AB strain rep1", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type AB strain", "GSM1273590", "GSM1273590: Wild type AB strain rep1; Danio rerio; RNA Seq", "GSM1273590", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273590", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "WT.fastq", "fastq", 898405760.0, 22460144.0, "GSM1273590 r1", "0:40", "A:227899706;C:221325355;G:214303297;T:234727455;N:149947", 40, null, null, null, 227899706, 221325355, 214303297, 234727455, 149947, "SRX381838", "SRS506055", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.941, null, 0.05403, null, 0.72023, null, 0.47159, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [37222, "SRR1035983", "SRX381837", "SRS506054", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "Wild type siblings rep3", "GSM1273589", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type siblings", "Wild type siblings rep3", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type siblings", "GSM1273589", "GSM1273589: Wild type siblings rep3; Danio rerio; RNA Seq", "GSM1273589", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273589", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "Sib3.fastq", "fastq", 969662040.0, 24241551.0, "GSM1273589 r1", "0:40", "A:249133974;C:234453313;G:228525325;T:257212156;N:337272", 40, null, null, null, 249133974, 234453313, 228525325, 257212156, 337272, "SRX381837", "SRS506054", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.93654, null, 0.06775, null, 0.7287, null, 0.47407, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [37223, "SRR1035982", "SRX381836", "SRS506053", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "Wild type siblings rep2", "GSM1273588", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type siblings", "Wild type siblings rep2", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type siblings", "GSM1273588", "GSM1273588: Wild type siblings rep2; Danio rerio; RNA Seq", "GSM1273588", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273588", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "Sib2.fastq", "fastq", 878040360.0, 21951009.0, "GSM1273588 r1", "0:40", "A:227146795;C:213249395;G:206995607;T:230550546;N:98017", 40, null, null, null, 227146795, 213249395, 206995607, 230550546, 98017, "SRX381836", "SRS506053", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.93985, null, 0.06787, null, 0.72535, null, 0.46201, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [37224, "SRR1035981", "SRX381835", "SRS506052", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "Wild type siblings rep1", "GSM1273587", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type siblings", "Wild type siblings rep1", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type siblings", "GSM1273587", "GSM1273587: Wild type siblings rep1; Danio rerio; RNA Seq", "GSM1273587", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273587", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "Sib1.fastq", "fastq", 915301760.0, 22882544.0, "GSM1273587 r1", "0:40", "A:237138826;C:220029947;G:215895418;T:241462118;N:775451", 40, null, null, null, 237138826, 220029947, 215895418, 241462118, 775451, "SRX381835", "SRS506052", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.90264, null, 0.06864, null, 0.72608, null, 0.47304, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [37225, "SRR1035980", "SRX381834", "SRS506051", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "rx3 /  rep3", "GSM1273586", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:rx3 / ", "rx3 /  rep3", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:rx3 / ", "GSM1273586", "GSM1273586: rx3 /  rep3; Danio rerio; RNA Seq", "GSM1273586", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273586", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "Eym3.fastq", "fastq", 897239440.0, 22430986.0, "GSM1273586 r1", "0:40", "A:229667647;C:217040944;G:214883750;T:235535742;N:111357", 40, null, null, null, 229667647, 217040944, 214883750, 235535742, 111357, "SRX381834", "SRS506051", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.93264, null, 0.06276, null, 0.7287, null, 0.46276, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [37226, "SRR1035979", "SRX381833", "SRS506050", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "rx3 /  rep2", "GSM1273585", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:rx3 / ", "rx3 /  rep2", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:rx3 / ", "GSM1273585", "GSM1273585: rx3 /  rep2; Danio rerio; RNA Seq", "GSM1273585", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273585", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "Eym2.fastq", "fastq", 834720720.0, 20868018.0, "GSM1273585 r1", "0:40", "A:208577702;C:206610978;G:201497582;T:217925002;N:109456", 40, null, null, null, 208577702, 206610978, 201497582, 217925002, 109456, "SRX381833", "SRS506050", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.9395, null, 0.06651, null, 0.72456, null, 0.47047, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [37227, "SRR1035978", "SRX381832", "SRS506049", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "rx3 /  rep1", "GSM1273584", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:rx3 / ", "rx3 /  rep1", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:rx3 / ", "GSM1273584", "GSM1273584: rx3 /  rep1; Danio rerio; RNA Seq", "GSM1273584", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273584", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "Eym1.fastq", "fastq", 1055937400.0, 26398435.0, "GSM1273584 r1", "0:40", "A:269230762;C:255997755;G:250156213;T:280406700;N:145970", 40, null, null, null, 269230762, 255997755, 250156213, 280406700, 145970, "SRX381832", "SRS506049", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.93973, null, 0.07114, null, 0.72072, null, 0.46482, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52143, "SRR8945523", "SRX5725653", "SRS4663723", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Npas4l KO 2", "GSM3733690", null, "tissue:Embryo|genotype:npas4l bns297/bns297", "Npas4l KO 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:npas4l bns297/bns297", "GSM3733690", "GSM3733690: Npas4l KO 2; Danio rerio; RNA Seq", "GSM3733690", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733690", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "NPAS4L-KO_2.fastq.gz", "fastq", 2188145091.0, 30480884.0, "GSM3733690 r1", "0:71.79 1:0", "A:565091244;C:556088129;G:587566739;T:479372691;N:26288", 71, 0, null, null, 565091244, 556088129, 587566739, 479372691, 26288, "SRX5725653", "SRS4663723", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93251, null, 0.36429, null, 0.79344, null, 0.7597, null, 70, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52144, "SRR8945522", "SRX5725652", "SRS4663722", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Npas4l KO 1", "GSM3733689", null, "tissue:Embryo|genotype:npas4l bns297/bns297", "Npas4l KO 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:npas4l bns297/bns297", "GSM3733689", "GSM3733689: Npas4l KO 1; Danio rerio; RNA Seq", "GSM3733689", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733689", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "NPAS4L-KO_1.fastq.gz", "fastq", 2433253496.0, 33687089.0, "GSM3733689 r1", "0:72.23 1:0", "A:593060668;C:644801659;G:698633749;T:496734812;N:22608", 72, 0, null, null, 593060668, 644801659, 698633749, 496734812, 22608, "SRX5725652", "SRS4663722", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.95463, null, 0.30956, null, 0.82254, null, 0.78357, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52145, "SRR8945521", "SRX5725651", "SRS4663720", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "WT 2", "GSM3733688", null, "tissue:Embryo|genotype:wild type", "WT 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:wild type", "GSM3733688", "GSM3733688: WT 2; Danio rerio; RNA Seq", "GSM3733688", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733688", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "WT_2.fastq.gz", "fastq", 2431837029.0, 33941204.0, "GSM3733688 r1", "0:71.65 1:0", "A:605500316;C:637722247;G:683241300;T:505342978;N:30188", 71, 0, null, null, 605500316, 637722247, 683241300, 505342978, 30188, "SRX5725651", "SRS4663720", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.94056, null, 0.3147, null, 0.80892, null, 0.75935, null, 37, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52146, "SRR8945520", "SRX5725650", "SRS4663721", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "WT 1", "GSM3733687", null, "tissue:Embryo|genotype:wild type", "WT 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:wild type", "GSM3733687", "GSM3733687: WT 1; Danio rerio; RNA Seq", "GSM3733687", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733687", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "WT_1.fastq.gz", "fastq", 2100118003.0, 29339428.0, "GSM3733687 r1", "0:71.58 1:0", "A:512913868;C:558713165;G:598879366;T:429576279;N:35325", 71, 0, null, null, 512913868, 558713165, 598879366, 429576279, 35325, "SRX5725650", "SRS4663721", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.94426, null, 0.30979, null, 0.80417, null, 0.76724, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52944, "SRR9609439", "SRX6372833", "SRS5033898", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 3", "GSM3909672", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909672", "GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq", "GSM3909672", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909672", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1283013300.0, 25660266.0, "GSM3909672 r1", "0:50", "A:339417002;C:304649204;G:297783450;T:341163644;N:0", 50, null, null, null, 339417002, 304649204, 297783450, 341163644, 0, "SRX6372833", "SRS5033898", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94342, null, 0.10559, null, 0.72401, null, 0.47431, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52945, "SRR9609438", "SRX6372832", "SRS5033897", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 2", "GSM3909671", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909671", "GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq", "GSM3909671", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909671", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1282475700.0, 25649514.0, "GSM3909671 r1", "0:50", "A:339635626;C:302447093;G:295507893;T:344885088;N:0", 50, null, null, null, 339635626, 302447093, 295507893, 344885088, 0, "SRX6372832", "SRS5033897", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94396, null, 0.10502, null, 0.71465, null, 0.47566, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52946, "SRR9609437", "SRX6372831", "SRS5033896", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 1", "GSM3909670", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909670", "GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq", "GSM3909670", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909670", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1147572700.0, 22951454.0, "GSM3909670 r1", "0:50", "A:300633532;C:273711082;G:268229512;T:304998574;N:0", 50, null, null, null, 300633532, 273711082, 268229512, 304998574, 0, "SRX6372831", "SRS5033896", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94418, null, 0.09965, null, 0.72746, null, 0.47644, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52947, "SRR9609436", "SRX6372830", "SRS5033895", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 3", "GSM3909669", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909669", "GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq", "GSM3909669", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909669", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1282414400.0, 25648288.0, "GSM3909669 r1", "0:50", "A:334687310;C:307161534;G:302070174;T:338495382;N:0", 50, null, null, null, 334687310, 307161534, 302070174, 338495382, 0, "SRX6372830", "SRS5033895", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94359, null, 0.09476, null, 0.72529, null, 0.47117, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52948, "SRR9609435", "SRX6372829", "SRS5033894", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 2", "GSM3909668", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909668", "GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq", "GSM3909668", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909668", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1281370000.0, 25627400.0, "GSM3909668 r1", "0:50", "A:335735118;C:306450529;G:298815464;T:340368889;N:0", 50, null, null, null, 335735118, 306450529, 298815464, 340368889, 0, "SRX6372829", "SRS5033894", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94338, null, 0.09412, null, 0.7204, null, 0.48662, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52949, "SRR9609434", "SRX6372828", "SRS5033893", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 1", "GSM3909667", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909667", "GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq", "GSM3909667", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909667", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1278504750.0, 25570095.0, "GSM3909667 r1", "0:50", "A:334370606;C:306252389;G:299065406;T:338816349;N:0", 50, null, null, null, 334370606, 306252389, 299065406, 338816349, 0, "SRX6372828", "SRS5033893", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94373, null, 0.09279, null, 0.7191, null, 0.48836, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52950, "SRR9609433", "SRX6372827", "SRS5033892", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 3", "GSM3909666", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909666", "GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq", "GSM3909666", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909666", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1284828600.0, 25696572.0, "GSM3909666 r1", "0:50", "A:340467505;C:302914392;G:291984238;T:349462465;N:0", 50, null, null, null, 340467505, 302914392, 291984238, 349462465, 0, "SRX6372827", "SRS5033892", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94288, null, 0.0963, null, 0.71713, null, 0.4793, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52951, "SRR9609432", "SRX6372826", "SRS5033891", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 2", "GSM3909665", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909665", "GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq", "GSM3909665", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909665", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1274433150.0, 25488663.0, "GSM3909665 r1", "0:50", "A:336050330;C:303141446;G:297353928;T:337887446;N:0", 50, null, null, null, 336050330, 303141446, 297353928, 337887446, 0, "SRX6372826", "SRS5033891", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94266, null, 0.0966, null, 0.72476, null, 0.47615, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52952, "SRR9609431", "SRX6372825", "SRS5033890", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 1", "GSM3909664", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909664", "GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq", "GSM3909664", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909664", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1278273350.0, 25565467.0, "GSM3909664 r1", "0:50", "A:336762127;C:304299745;G:297929933;T:339281545;N:0", 50, null, null, null, 336762127, 304299745, 297929933, 339281545, 0, "SRX6372825", "SRS5033890", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94207, null, 0.09472, null, 0.72642, null, 0.47988, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55351, "SRR10312407", "SRX7023627", "SRS5544403", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 homo 15som 3", "GSM4131107", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "etv2 homo 15som 3", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "GSM4131107", "GSM4131107: etv2 homo 15som 3; Danio rerio; RNA Seq", "GSM4131107", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_M_15som_3_1.fq.gz Gal4_M_15som_3_2.fq.gz", "fastq fastq", 6761255100.0, 22537517.0, "GSM4131107 r1", "0:150 1:150", "A:1866486620;C:1515599328;G:1552923507;T:1825555968;N:689677", 150, 150, null, null, 1866486620, 1515599328, 1552923507, 1825555968, 689677, "SRX7023627", "SRS5544403", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.92459, 0.9271, 0.10249, 0.10409, 0.71796, 0.73742, 0.47946, 0.48392, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55352, "SRR10312406", "SRX7023626", "SRS5544402", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 homo 15som 2", "GSM4131106", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "etv2 homo 15som 2", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "GSM4131106", "GSM4131106: etv2 homo 15som 2; Danio rerio; RNA Seq", "GSM4131106", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_M_15som_2_1.fq.gz Gal4_M_15som_2_2.fq.gz", "fastq fastq", 7981387800.0, 26604626.0, "GSM4131106 r1", "0:150 1:150", "A:2202882836;C:1794183789;G:1829145498;T:2155175677;N:0", 150, 150, null, null, 2202882836, 1794183789, 1829145498, 2155175677, 0, "SRX7023626", "SRS5544402", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.92725, 0.92934, 0.10292, 0.10466, 0.71683, 0.73229, 0.47835, 0.49406, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55353, "SRR10312405", "SRX7023625", "SRS5544401", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 homo 15som 1", "GSM4131105", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "etv2 homo 15som 1", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "GSM4131105", "GSM4131105: etv2 homo 15som 1; Danio rerio; RNA Seq", "GSM4131105", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_M_15som_1_1.fq.gz Gal4_M_15som_1_2.fq.gz", "fastq fastq", 7603849500.0, 25346165.0, "GSM4131105 r1", "0:150 1:150", "A:2090131691;C:1715529001;G:1749529239;T:2048659569;N:0", 150, 150, null, null, 2090131691, 1715529001, 1749529239, 2048659569, 0, "SRX7023625", "SRS5544401", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.93146, 0.93272, 0.09858, 0.10047, 0.71187, 0.7289, 0.47673, 0.4841, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55354, "SRR10312404", "SRX7023624", "SRS5544400", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 het 15som 3", "GSM4131104", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite", "etv2 het 15som 3", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite", "GSM4131104", "GSM4131104: etv2 het 15som 3; Danio rerio; RNA Seq", "GSM4131104", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_S_15som_3_1.fq.gz Gal4_S_15som_3_2.fq.gz", "fastq fastq", 7066336800.0, 23554456.0, "GSM4131104 r1", "0:150 1:150", "A:1939539558;C:1600239608;G:1629483507;T:1896228696;N:845431", 150, 150, null, null, 1939539558, 1600239608, 1629483507, 1896228696, 845431, "SRX7023624", "SRS5544400", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.93054, 0.93331, 0.09158, 0.09266, 0.71729, 0.72983, 0.47907, 0.4826, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55355, "SRR10312403", "SRX7023623", "SRS5544399", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 het 15som 2", "GSM4131103", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite", "etv2 het 15som 2", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite", "GSM4131103", "GSM4131103: etv2 het 15som 2; Danio rerio; RNA Seq", "GSM4131103", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_S_15som_2_2.fq.gz Gal4_S_15som_2_1.fq.gz", "fastq fastq", 6470013600.0, 21566712.0, "GSM4131103 r1", "0:150 1:150", "A:1776945744;C:1463614010;G:1487591153;T:1740908499;N:954194", 150, 150, null, null, 1776945744, 1463614010, 1487591153, 1740908499, 954194, "SRX7023623", "SRS5544399", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.9287, 0.92958, 0.09528, 0.09614, 0.71735, 0.73265, 0.48939, 0.47903, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55356, "SRR10312402", "SRX7023622", "SRS5544398", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 het 15som 1", "GSM4131102", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite", "etv2 het 15som 1", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite", "GSM4131102", "GSM4131102: etv2 het 15som 1; Danio rerio; RNA Seq", "GSM4131102", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_S_15som_1_1.fq.gz Gal4_S_15som_1_2.fq.gz", "fastq fastq", 6901490400.0, 23004968.0, "GSM4131102 r1", "0:150 1:150", "A:1890965544;C:1565806757;G:1593741246;T:1850119873;N:856980", 150, 150, null, null, 1890965544, 1565806757, 1593741246, 1850119873, 856980, "SRX7023622", "SRS5544398", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.93226, 0.93447, 0.08708, 0.08854, 0.72163, 0.7359, 0.479, 0.48316, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65712, "SRR15600966", "SRX11898455", "SRS9909637", "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 12h rep 3", "GSM5535071", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h rep 3", "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:12hpf", "GSM5535071", "GSM5535071: Adar OE 12h rep 3; Danio rerio; RNA Seq", "GSM5535071", 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:GSM5535071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-OE_S8_L001_R1_001.fastq.gz C-12h-OE_S8_L001_R2_001.fastq.gz", "fastq fastq", 762794064.0, 5018382.0, "GSM5535071 r1", "0:76 1:76", "A:190096300;C:189646060;G:193984365;T:188324693;N:742646", 76, 76, null, null, 190096300, 189646060, 193984365, 188324693, 742646, "SRX11898455", "SRS9909637", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93757, 0.94301, 0.16502, 0.16402, 0.72665, 0.72673, 0.50013, 0.50746, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65713, "SRR15600967", "SRX11898455", "SRS9909637", "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 12h rep 3", "GSM5535071", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h rep 3", "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:12hpf", "GSM5535071", "GSM5535071: Adar OE 12h rep 3; Danio rerio; RNA Seq", "GSM5535071", 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:GSM5535071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-OE_S8_L002_R1_001.fastq.gz C-12h-OE_S8_L002_R2_001.fastq.gz", "fastq fastq", 766188528.0, 5040714.0, "GSM5535071 r2", "0:76 1:76", "A:191123733;C:190497618;G:194623391;T:189218434;N:725352", 76, 76, null, null, 191123733, 190497618, 194623391, 189218434, 725352, "SRX11898455", "SRS9909637", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93846, 0.94266, 0.16448, 0.16232, 0.72423, 0.72525, 0.50393, 0.50481, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65714, "SRR15600968", "SRX11898455", "SRS9909637", "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 12h rep 3", "GSM5535071", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h rep 3", "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:12hpf", "GSM5535071", "GSM5535071: Adar OE 12h rep 3; Danio rerio; RNA Seq", "GSM5535071", 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:GSM5535071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-OE_S8_L003_R1_001.fastq.gz C-12h-OE_S8_L003_R2_001.fastq.gz", "fastq fastq", 767910536.0, 5052043.0, "GSM5535071 r3", "0:76 1:76", "A:191655261;C:190952201;G:195252442;T:189697946;N:352686", 76, 76, null, null, 191655261, 190952201, 195252442, 189697946, 352686, "SRX11898455", "SRS9909637", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.938, 0.9419, 0.16708, 0.16477, 0.72742, 0.72788, 0.50363, 0.50838, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65715, "SRR15600969", "SRX11898455", "SRS9909637", "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 12h rep 3", "GSM5535071", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h rep 3", "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:12hpf", "GSM5535071", "GSM5535071: Adar OE 12h rep 3; Danio rerio; RNA Seq", "GSM5535071", 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:GSM5535071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-OE_S8_L004_R1_001.fastq.gz C-12h-OE_S8_L004_R2_001.fastq.gz", "fastq fastq", 755981272.0, 4973561.0, "GSM5535071 r4", "0:76 1:76", "A:188733355;C:187911263;G:192111735;T:186831998;N:392921", 76, 76, null, null, 188733355, 187911263, 192111735, 186831998, 392921, "SRX11898455", "SRS9909637", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93834, 0.94271, 0.16362, 0.16331, 0.72689, 0.72636, 0.49523, 0.50512, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65716, "SRR15600962", "SRX11898454", "SRS9909636", "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 12h rep 2", "GSM5535070", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535070", "GSM5535070: Adar OE 12h rep 2; Danio rerio; RNA Seq", "GSM5535070", 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:GSM5535070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-OE_S5_L001_R1_001.fastq.gz B-12h-OE_S5_L001_R2_001.fastq.gz", "fastq fastq", 839086360.0, 5520305.0, "GSM5535070 r1", "0:76 1:76", "A:212155130;C:205028383;G:209332704;T:211766587;N:803556", 76, 76, null, null, 212155130, 205028383, 209332704, 211766587, 803556, "SRX11898454", "SRS9909636", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92524, 0.92936, 0.26529, 0.2613, 0.70682, 0.70849, 0.52844, 0.5414, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65717, "SRR15600963", "SRX11898454", "SRS9909636", "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 12h rep 2", "GSM5535070", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535070", "GSM5535070: Adar OE 12h rep 2; Danio rerio; RNA Seq", "GSM5535070", 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:GSM5535070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-OE_S5_L002_R1_001.fastq.gz B-12h-OE_S5_L002_R2_001.fastq.gz", "fastq fastq", 842040480.0, 5539740.0, "GSM5535070 r2", "0:76 1:76", "A:213107507;C:205706191;G:209800940;T:212630355;N:795487", 76, 76, null, null, 213107507, 205706191, 209800940, 212630355, 795487, "SRX11898454", "SRS9909636", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92569, 0.92777, 0.26536, 0.26077, 0.70563, 0.70755, 0.5394, 0.5445, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65718, "SRR15600964", "SRX11898454", "SRS9909636", "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 12h rep 2", "GSM5535070", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535070", "GSM5535070: Adar OE 12h rep 2; Danio rerio; RNA Seq", "GSM5535070", 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:GSM5535070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-OE_S5_L003_R1_001.fastq.gz B-12h-OE_S5_L003_R2_001.fastq.gz", "fastq fastq", 845886688.0, 5565044.0, "GSM5535070 r3", "0:76 1:76", "A:214160965;C:206711710;G:210987325;T:213635533;N:391155", 76, 76, null, null, 214160965, 206711710, 210987325, 213635533, 391155, "SRX11898454", "SRS9909636", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92456, 0.92847, 0.26566, 0.26144, 0.70603, 0.70853, 0.52644, 0.53762, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65719, "SRR15600965", "SRX11898454", "SRS9909636", "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 12h rep 2", "GSM5535070", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535070", "GSM5535070: Adar OE 12h rep 2; Danio rerio; RNA Seq", "GSM5535070", 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:GSM5535070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-OE_S5_L004_R1_001.fastq.gz B-12h-OE_S5_L004_R2_001.fastq.gz", "fastq fastq", 832192704.0, 5474952.0, "GSM5535070 r4", "0:76 1:76", "A:210790432;C:203228024;G:207377096;T:210366212;N:430940", 76, 76, null, null, 210790432, 203228024, 207377096, 210366212, 430940, "SRX11898454", "SRS9909636", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92504, 0.92839, 0.26518, 0.26088, 0.7067, 0.70905, 0.53807, 0.54235, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65720, "SRR15600958", "SRX11898453", "SRS9909635", "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 12h rep 1", "GSM5535069", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535069", "GSM5535069: Adar OE 12h rep 1; Danio rerio; RNA Seq", "GSM5535069", 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:GSM5535069", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-OE_S11_L001_R1_001.fastq.gz A-12h-OE_S11_L001_R2_001.fastq.gz", "fastq fastq", 617487232.0, 4062416.0, "GSM5535069 r1", "0:76 1:76", "A:157003609;C:148811718;G:154097069;T:156986022;N:588814", 76, 76, null, null, 157003609, 148811718, 154097069, 156986022, 588814, "SRX11898453", "SRS9909635", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92221, 0.92801, 0.26791, 0.2668, 0.70597, 0.70838, 0.48916, 0.49335, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65721, "SRR15600959", "SRX11898453", "SRS9909635", "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 12h rep 1", "GSM5535069", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535069", "GSM5535069: Adar OE 12h rep 1; Danio rerio; RNA Seq", "GSM5535069", 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:GSM5535069", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-OE_S11_L002_R1_001.fastq.gz A-12h-OE_S11_L002_R2_001.fastq.gz", "fastq fastq", 617705656.0, 4063853.0, "GSM5535069 r2", "0:76 1:76", "A:157241656;C:148829493;G:153930442;T:157129658;N:574407", 76, 76, null, null, 157241656, 148829493, 153930442, 157129658, 574407, "SRX11898453", "SRS9909635", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92283, 0.92898, 0.26661, 0.26667, 0.70674, 0.70981, 0.48563, 0.47092, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65722, "SRR15600960", "SRX11898453", "SRS9909635", "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 12h rep 1", "GSM5535069", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535069", "GSM5535069: Adar OE 12h rep 1; Danio rerio; RNA Seq", "GSM5535069", 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:GSM5535069", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-OE_S11_L003_R1_001.fastq.gz A-12h-OE_S11_L003_R2_001.fastq.gz", "fastq fastq", 620843544.0, 4084497.0, "GSM5535069 r3", "0:76 1:76", "A:158128564;C:149641460;G:154848619;T:157936393;N:288508", 76, 76, null, null, 158128564, 149641460, 154848619, 157936393, 288508, "SRX11898453", "SRS9909635", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92314, 0.9279, 0.26489, 0.26392, 0.70548, 0.70786, 0.49058, 0.47762, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65723, "SRR15600961", "SRX11898453", "SRS9909635", "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 12h rep 1", "GSM5535069", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar OE 12h 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:12hpf", "GSM5535069", "GSM5535069: Adar OE 12h rep 1; Danio rerio; RNA Seq", "GSM5535069", 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:GSM5535069", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-OE_S11_L004_R1_001.fastq.gz A-12h-OE_S11_L004_R2_001.fastq.gz", "fastq fastq", 609650112.0, 4010856.0, "GSM5535069 r4", "0:76 1:76", "A:155280334;C:146899976;G:152009494;T:155149257;N:311051", 76, 76, null, null, 155280334, 146899976, 152009494, 155149257, 311051, "SRX11898453", "SRS9909635", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92323, 0.92778, 0.26748, 0.26609, 0.7068, 0.70849, 0.48633, 0.49127, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65724, "SRR15600954", "SRX11898452", "SRS9909634", "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 12h rep 3", "GSM5535068", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h rep 3", "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:12hpf", "GSM5535068", "GSM5535068: Adar MO 12h rep 3; Danio rerio; RNA Seq", "GSM5535068", 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:GSM5535068", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-MO_S9_L001_R1_001.fastq.gz C-12h-MO_S9_L001_R2_001.fastq.gz", "fastq fastq", 791451536.0, 5206918.0, "GSM5535068 r1", "0:76 1:76", "A:191854060;C:201162777;G:207858389;T:189828642;N:747668", 76, 76, null, null, 191854060, 201162777, 207858389, 189828642, 747668, "SRX11898452", "SRS9909634", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.91033, 0.91964, 0.17302, 0.17119, 0.71875, 0.71918, 0.51851, 0.52065, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65725, "SRR15600955", "SRX11898452", "SRS9909634", "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 12h rep 3", "GSM5535068", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h rep 3", "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:12hpf", "GSM5535068", "GSM5535068: Adar MO 12h rep 3; Danio rerio; RNA Seq", "GSM5535068", 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:GSM5535068", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-MO_S9_L002_R1_001.fastq.gz C-12h-MO_S9_L002_R2_001.fastq.gz", "fastq fastq", 784453608.0, 5160879.0, "GSM5535068 r2", "0:76 1:76", "A:190462386;C:199292667;G:205615385;T:188336507;N:746663", 76, 76, null, null, 190462386, 199292667, 205615385, 188336507, 746663, "SRX11898452", "SRS9909634", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.91115, 0.92157, 0.17267, 0.1726, 0.72109, 0.72239, 0.51728, 0.51726, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65726, "SRR15600956", "SRX11898452", "SRS9909634", "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 12h rep 3", "GSM5535068", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h rep 3", "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:12hpf", "GSM5535068", "GSM5535068: Adar MO 12h rep 3; Danio rerio; RNA Seq", "GSM5535068", 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:GSM5535068", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-MO_S9_L003_R1_001.fastq.gz C-12h-MO_S9_L003_R2_001.fastq.gz", "fastq fastq", 796941776.0, 5243038.0, "GSM5535068 r3", "0:76 1:76", "A:193533711;C:202544366;G:209159326;T:191336024;N:368349", 76, 76, null, null, 193533711, 202544366, 209159326, 191336024, 368349, "SRX11898452", "SRS9909634", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.9117, 0.9207, 0.17417, 0.17328, 0.71786, 0.7207, 0.51697, 0.52533, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65727, "SRR15600957", "SRX11898452", "SRS9909634", "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 12h rep 3", "GSM5535068", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h rep 3", "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:12hpf", "GSM5535068", "GSM5535068: Adar MO 12h rep 3; Danio rerio; RNA Seq", "GSM5535068", 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:GSM5535068", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-MO_S9_L004_R1_001.fastq.gz C-12h-MO_S9_L004_R2_001.fastq.gz", "fastq fastq", 775028848.0, 5098874.0, "GSM5535068 r4", "0:76 1:76", "A:188415416;C:196744039;G:203147300;T:186326840;N:395253", 76, 76, null, null, 188415416, 196744039, 203147300, 186326840, 395253, "SRX11898452", "SRS9909634", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.91249, 0.92074, 0.17336, 0.17294, 0.71965, 0.72188, 0.51754, 0.52395, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65728, "SRR15600950", "SRX11898451", "SRS9909633", "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 12h rep 2", "GSM5535067", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535067", "GSM5535067: Adar MO 12h rep 2; Danio rerio; RNA Seq", "GSM5535067", 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:GSM5535067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-MO_S6_L001_R1_001.fastq.gz B-12h-MO_S6_L001_R2_001.fastq.gz", "fastq fastq", 799553592.0, 5260221.0, "GSM5535067 r1", "0:76 1:76", "A:195752280;C:201769131;G:206861841;T:194397821;N:772519", 76, 76, null, null, 195752280, 201769131, 206861841, 194397821, 772519, "SRX11898451", "SRS9909633", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93325, 0.93431, 0.23563, 0.23114, 0.715, 0.71707, 0.55754, 0.55116, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65729, "SRR15600951", "SRX11898451", "SRS9909633", "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 12h rep 2", "GSM5535067", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535067", "GSM5535067: Adar MO 12h rep 2; Danio rerio; RNA Seq", "GSM5535067", 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:GSM5535067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-MO_S6_L002_R1_001.fastq.gz B-12h-MO_S6_L002_R2_001.fastq.gz", "fastq fastq", 799637800.0, 5260775.0, "GSM5535067 r2", "0:76 1:76", "A:196056213;C:201708589;G:206574784;T:194543686;N:754528", 76, 76, null, null, 196056213, 201708589, 206574784, 194543686, 754528, "SRX11898451", "SRS9909633", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93289, 0.93497, 0.23546, 0.23216, 0.71153, 0.71575, 0.54753, 0.56579, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65730, "SRR15600952", "SRX11898451", "SRS9909633", "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 12h rep 2", "GSM5535067", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535067", "GSM5535067: Adar MO 12h rep 2; Danio rerio; RNA Seq", "GSM5535067", 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:GSM5535067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-MO_S6_L003_R1_001.fastq.gz B-12h-MO_S6_L003_R2_001.fastq.gz", "fastq fastq", 804791968.0, 5294684.0, "GSM5535067 r3", "0:76 1:76", "A:197427156;C:203086180;G:208091929;T:195819282;N:367421", 76, 76, null, null, 197427156, 203086180, 208091929, 195819282, 367421, "SRX11898451", "SRS9909633", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93236, 0.93446, 0.23307, 0.22857, 0.71437, 0.71492, 0.58252, 0.57484, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65731, "SRR15600953", "SRX11898451", "SRS9909633", "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 12h rep 2", "GSM5535067", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535067", "GSM5535067: Adar MO 12h rep 2; Danio rerio; RNA Seq", "GSM5535067", 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:GSM5535067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-MO_S6_L004_R1_001.fastq.gz B-12h-MO_S6_L004_R2_001.fastq.gz", "fastq fastq", 789674808.0, 5195229.0, "GSM5535067 r4", "0:76 1:76", "A:193784929;C:199145966;G:204032387;T:192303387;N:408139", 76, 76, null, null, 193784929, 199145966, 204032387, 192303387, 408139, "SRX11898451", "SRS9909633", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.93313, 0.93701, 0.23443, 0.23023, 0.71285, 0.71541, 0.56342, 0.59304, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65732, "SRR15600946", "SRX11898450", "SRS9909632", "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 12h rep 1", "GSM5535066", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535066", "GSM5535066: Adar MO 12h rep 1; Danio rerio; RNA Seq", "GSM5535066", 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:GSM5535066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-MO_S12_L001_R1_001.fastq.gz A-12h-MO_S12_L001_R2_001.fastq.gz", "fastq fastq", 765583112.0, 5036731.0, "GSM5535066 r1", "0:76 1:76", "A:183140717;C:197120320;G:202313379;T:182273627;N:735069", 76, 76, null, null, 183140717, 197120320, 202313379, 182273627, 735069, "SRX11898450", "SRS9909632", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.88403, 0.89031, 0.17028, 0.16932, 0.73359, 0.73464, 0.55121, 0.56289, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65733, "SRR15600947", "SRX11898450", "SRS9909632", "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 12h rep 1", "GSM5535066", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535066", "GSM5535066: Adar MO 12h rep 1; Danio rerio; RNA Seq", "GSM5535066", 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:GSM5535066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-MO_S12_L002_R1_001.fastq.gz A-12h-MO_S12_L002_R2_001.fastq.gz", "fastq fastq", 768103728.0, 5053314.0, "GSM5535066 r2", "0:76 1:76", "A:184010664;C:197750259;G:202683705;T:182936167;N:722933", 76, 76, null, null, 184010664, 197750259, 202683705, 182936167, 722933, "SRX11898450", "SRS9909632", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.88456, 0.89086, 0.17068, 0.1711, 0.73316, 0.73541, 0.54996, 0.55548, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65734, "SRR15600948", "SRX11898450", "SRS9909632", "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 12h rep 1", "GSM5535066", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535066", "GSM5535066: Adar MO 12h rep 1; Danio rerio; RNA Seq", "GSM5535066", 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:GSM5535066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-MO_S12_L003_R1_001.fastq.gz A-12h-MO_S12_L003_R2_001.fastq.gz", "fastq fastq", 771361848.0, 5074749.0, "GSM5535066 r3", "0:76 1:76", "A:184885659;C:198637482;G:203702404;T:183781237;N:355066", 76, 76, null, null, 184885659, 198637482, 203702404, 183781237, 355066, "SRX11898450", "SRS9909632", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.8841, 0.88942, 0.17054, 0.17088, 0.73196, 0.73464, 0.55591, 0.55852, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65735, "SRR15600949", "SRX11898450", "SRS9909632", "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 12h rep 1", "GSM5535066", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Adar MO 12h 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:12hpf", "GSM5535066", "GSM5535066: Adar MO 12h rep 1; Danio rerio; RNA Seq", "GSM5535066", 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:GSM5535066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-MO_S12_L004_R1_001.fastq.gz A-12h-MO_S12_L004_R2_001.fastq.gz", "fastq fastq", 758633976.0, 4991013.0, "GSM5535066 r4", "0:76 1:76", "A:181900606;C:195243401;G:200256020;T:180846675;N:387274", 76, 76, null, null, 181900606, 195243401, 200256020, 180846675, 387274, "SRX11898450", "SRS9909632", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.88502, 0.88969, 0.1721, 0.17192, 0.73452, 0.73639, 0.54744, 0.55692, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65736, "SRR15600942", "SRX11898449", "SRS9909631", "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 12hpf rep 3", "GSM5535065", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf rep 3", "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:12hpf", "GSM5535065", "GSM5535065: Control 12hpf rep 3; Danio rerio; RNA Seq", "GSM5535065", 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:GSM5535065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-ctrl_S7_L001_R1_001.fastq.gz C-12h-ctrl_S7_L001_R2_001.fastq.gz", "fastq fastq", 673770400.0, 4432700.0, "GSM5535065 r1", "0:76 1:76", "A:163247662;C:171610482;G:176524847;T:161735077;N:652332", 76, 76, null, null, 163247662, 171610482, 176524847, 161735077, 652332, "SRX11898449", "SRS9909631", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.89926, 0.90991, 0.16896, 0.16975, 0.73338, 0.73279, 0.49853, 0.49939, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65737, "SRR15600943", "SRX11898449", "SRS9909631", "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 12hpf rep 3", "GSM5535065", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf rep 3", "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:12hpf", "GSM5535065", "GSM5535065: Control 12hpf rep 3; Danio rerio; RNA Seq", "GSM5535065", 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:GSM5535065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-ctrl_S7_L002_R1_001.fastq.gz C-12h-ctrl_S7_L002_R2_001.fastq.gz", "fastq fastq", 673106160.0, 4428330.0, "GSM5535065 r2", "0:76 1:76", "A:163330144;C:171338168;G:176077991;T:161731544;N:628313", 76, 76, null, null, 163330144, 171338168, 176077991, 161731544, 628313, "SRX11898449", "SRS9909631", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.89992, 0.91056, 0.17088, 0.17095, 0.7316, 0.73206, 0.49369, 0.50003, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65738, "SRR15600944", "SRX11898449", "SRS9909631", "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 12hpf rep 3", "GSM5535065", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf rep 3", "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:12hpf", "GSM5535065", "GSM5535065: Control 12hpf rep 3; Danio rerio; RNA Seq", "GSM5535065", 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:GSM5535065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-ctrl_S7_L003_R1_001.fastq.gz C-12h-ctrl_S7_L003_R2_001.fastq.gz", "fastq fastq", 677875920.0, 4459710.0, "GSM5535065 r3", "0:76 1:76", "A:164572649;C:172611262;G:177413100;T:162963537;N:315372", 76, 76, null, null, 164572649, 172611262, 177413100, 162963537, 315372, "SRX11898449", "SRS9909631", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.90035, 0.9095, 0.17008, 0.17027, 0.73038, 0.7303, 0.49422, 0.49918, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65739, "SRR15600945", "SRX11898449", "SRS9909631", "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 12hpf rep 3", "GSM5535065", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf rep 3", "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:12hpf", "GSM5535065", "GSM5535065: Control 12hpf rep 3; Danio rerio; RNA Seq", "GSM5535065", 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:GSM5535065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "C-12h-ctrl_S7_L004_R1_001.fastq.gz C-12h-ctrl_S7_L004_R2_001.fastq.gz", "fastq fastq", 664591576.0, 4372313.0, "GSM5535065 r4", "0:76 1:76", "A:161448836;C:169078740;G:173843248;T:159875972;N:344780", 76, 76, null, null, 161448836, 169078740, 173843248, 159875972, 344780, "SRX11898449", "SRS9909631", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.89878, 0.90973, 0.16854, 0.16873, 0.73184, 0.73162, 0.47421, 0.49772, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65740, "SRR15600938", "SRX11898448", "SRS9909630", "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 12hpf rep 2", "GSM5535064", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535064", "GSM5535064: Control 12hpf rep 2; Danio rerio; RNA Seq", "GSM5535064", 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:GSM5535064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-ctrl_S4_L001_R1_001.fastq.gz B-12h-ctrl_S4_L001_R2_001.fastq.gz", "fastq fastq", 883167272.0, 5810311.0, "GSM5535064 r1", "0:76 1:76", "A:221947855;C:217672447;G:221412656;T:221284287;N:850027", 76, 76, null, null, 221947855, 217672447, 221412656, 221284287, 850027, "SRX11898448", "SRS9909630", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92803, 0.9316, 0.24907, 0.2444, 0.71047, 0.71027, 0.53112, 0.53633, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65741, "SRR15600939", "SRX11898448", "SRS9909630", "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 12hpf rep 2", "GSM5535064", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535064", "GSM5535064: Control 12hpf rep 2; Danio rerio; RNA Seq", "GSM5535064", 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:GSM5535064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-ctrl_S4_L002_R1_001.fastq.gz B-12h-ctrl_S4_L002_R2_001.fastq.gz", "fastq fastq", 879560768.0, 5786584.0, "GSM5535064 r2", "0:76 1:76", "A:221264286;C:216696577;G:220257149;T:220511260;N:831496", 76, 76, null, null, 221264286, 216696577, 220257149, 220511260, 831496, "SRX11898448", "SRS9909630", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92635, 0.9306, 0.24857, 0.2441, 0.71338, 0.71453, 0.53145, 0.53643, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65742, "SRR15600940", "SRX11898448", "SRS9909630", "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 12hpf rep 2", "GSM5535064", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535064", "GSM5535064: Control 12hpf rep 2; Danio rerio; RNA Seq", "GSM5535064", 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:GSM5535064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-ctrl_S4_L003_R1_001.fastq.gz B-12h-ctrl_S4_L003_R2_001.fastq.gz", "fastq fastq", 889087672.0, 5849261.0, "GSM5535064 r3", "0:76 1:76", "A:223770316;C:219113112;G:222845687;T:222949178;N:409379", 76, 76, null, null, 223770316, 219113112, 222845687, 222949178, 409379, "SRX11898448", "SRS9909630", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92538, 0.93049, 0.24853, 0.2461, 0.7109, 0.71169, 0.5323, 0.53966, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65743, "SRR15600941", "SRX11898448", "SRS9909630", "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 12hpf rep 2", "GSM5535064", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535064", "GSM5535064: Control 12hpf rep 2; Danio rerio; RNA Seq", "GSM5535064", 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:GSM5535064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "B-12h-ctrl_S4_L004_R1_001.fastq.gz B-12h-ctrl_S4_L004_R2_001.fastq.gz", "fastq fastq", 869862864.0, 5722782.0, "GSM5535064 r4", "0:76 1:76", "A:219020116;C:214261442;G:217835304;T:218299707;N:446295", 76, 76, null, null, 219020116, 214261442, 217835304, 218299707, 446295, "SRX11898448", "SRS9909630", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92705, 0.93072, 0.24912, 0.24506, 0.7106, 0.71171, 0.53191, 0.53778, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65744, "SRR15600934", "SRX11898447", "SRS9909629", "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 12hpf rep 1", "GSM5535063", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535063", "GSM5535063: Control 12hpf rep 1; Danio rerio; RNA Seq", "GSM5535063", 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:GSM5535063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-ctrl_S10_L001_R1_001.fastq.gz A-12h-ctrl_S10_L001_R2_001.fastq.gz", "fastq fastq", 737175984.0, 4849842.0, "GSM5535063 r1", "0:76 1:76", "A:170563497;C:196023890;G:203838842;T:166043384;N:706371", 76, 76, null, null, 170563497, 196023890, 203838842, 166043384, 706371, "SRX11898447", "SRS9909629", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92432, 0.93141, 0.1447, 0.14536, 0.76104, 0.76382, 0.54346, 0.53318, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65745, "SRR15600935", "SRX11898447", "SRS9909629", "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 12hpf rep 1", "GSM5535063", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535063", "GSM5535063: Control 12hpf rep 1; Danio rerio; RNA Seq", "GSM5535063", 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:GSM5535063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-ctrl_S10_L002_R1_001.fastq.gz A-12h-ctrl_S10_L002_R2_001.fastq.gz", "fastq fastq", 738097256.0, 4855903.0, "GSM5535063 r2", "0:76 1:76", "A:171255393;C:196182129;G:203575129;T:166395040;N:689565", 76, 76, null, null, 171255393, 196182129, 203575129, 166395040, 689565, "SRX11898447", "SRS9909629", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.9252, 0.93062, 0.14419, 0.14324, 0.76114, 0.76483, 0.54093, 0.53521, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65746, "SRR15600936", "SRX11898447", "SRS9909629", "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 12hpf rep 1", "GSM5535063", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535063", "GSM5535063: Control 12hpf rep 1; Danio rerio; RNA Seq", "GSM5535063", 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:GSM5535063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-ctrl_S10_L003_R1_001.fastq.gz A-12h-ctrl_S10_L003_R2_001.fastq.gz", "fastq fastq", 740461312.0, 4871456.0, "GSM5535063 r3", "0:76 1:76", "A:171905507;C:196906899;G:204369509;T:166930886;N:348511", 76, 76, null, null, 171905507, 196906899, 204369509, 166930886, 348511, "SRX11898447", "SRS9909629", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92363, 0.93046, 0.14687, 0.14701, 0.76163, 0.7666, 0.53554, 0.53843, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [65747, "SRR15600937", "SRX11898447", "SRS9909629", "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 12hpf rep 1", "GSM5535063", null, "source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:12hpf", "Control 12hpf 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:12hpf", "GSM5535063", "GSM5535063: Control 12hpf rep 1; Danio rerio; RNA Seq", "GSM5535063", 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:GSM5535063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP333957", null, null, "A-12h-ctrl_S10_L004_R1_001.fastq.gz A-12h-ctrl_S10_L004_R2_001.fastq.gz", "fastq fastq", 727698784.0, 4787492.0, "GSM5535063 r4", "0:76 1:76", "A:169032340;C:193287471;G:200810885;T:164195909;N:372179", 76, 76, null, null, 169032340, 193287471, 200810885, 164195909, 372179, "SRX11898447", "SRS9909629", "SRA1283368", "GEO", "Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.92507, 0.93154, 0.1437, 0.14387, 0.76195, 0.76455, 0.53799, 0.5357, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "Poland", "2021-08-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [68644, "SRR18090806", "SRX14241863", "SRS12062497", "SRP360814", "PRJNA809026", "Competition for H2A.Z underlies the developmental impacts of repetitive element de repression", "GSE197131", "Transcriptome Analysis", "The histone variant H2A.Z is central to early embryonic development  determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "H2A.ZmCherry 5AzadC 12hpf totalRNA Rep3", "GSM5909698", null, "tissue:zebrafish embryos|developmental stage:12hpf overexpression|treatment:5AzadC|geo loc name:missing|collection date:missing", "H2A.ZmCherry 5AzadC 12hpf totalRNA Rep3", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. Differentially expressed genes were identified using DESeq2 v1.22.2 in R/3.5.1 Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters:   normalizeUsing RPKM   binSize 10 Genome build: Zv11 Supplementary files format and content: bigWig files and txt files", "zebrafish embryos", "Newly fertilized eggs were collected immediately post spawning  and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza dC   or with 0.1% DMSO for control group.", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", "Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle", "developmental stage:12hpf overexpression|treatment:5AzadC", "GSM5909698", "GSM5909698: H2A.ZmCherry 5AzadC 12hpf totalRNA Rep3; Danio rerio; RNA Seq", "GSM5909698 r1", "GSM5909698", "1", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP360814", null, "loader:fastq load.py", "H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep3_Clean_Data1.fq.gz H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep3_Clean_Data2.fq.gz", "fastq fastq", 8684470911.0, 31260993.0, "GSM5909698 r1", "0:138.93 1:138.88", "A:1121161752;C:3177212748;G:3291082795;T:1094901062;N:112554", 138, 138, null, null, 1121161752, 3177212748, 3291082795, 1094901062, 112554, "SRX14241863", "SRS12062497", "SRA1376914", "Biomedical Genetics, University of Rochester Medical Center", "Biomedical Genetics, University of Rochester Medical Center", 2, 0.97388, 0.98144, 0.06684, 0.06664, 0.87856, 0.87815, 0.89545, 0.89835, 142, 142, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-21", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68645, "SRR18090807", "SRX14241862", "SRS12062496", "SRP360814", "PRJNA809026", "Competition for H2A.Z underlies the developmental impacts of repetitive element de repression", "GSE197131", "Transcriptome Analysis", "The histone variant H2A.Z is central to early embryonic development  determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "H2A.ZmCherry 5AzadC 12hpf totalRNA Rep2", "GSM5909697", null, "tissue:zebrafish embryos|developmental stage:12hpf overexpression|treatment:5AzadC|geo loc name:missing|collection date:missing", "H2A.ZmCherry 5AzadC 12hpf totalRNA Rep2", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. Differentially expressed genes were identified using DESeq2 v1.22.2 in R/3.5.1 Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters:   normalizeUsing RPKM   binSize 10 Genome build: Zv11 Supplementary files format and content: bigWig files and txt files", "zebrafish embryos", "Newly fertilized eggs were collected immediately post spawning  and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza dC   or with 0.1% DMSO for control group.", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", "Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle", "developmental stage:12hpf overexpression|treatment:5AzadC", "GSM5909697", "GSM5909697: H2A.ZmCherry 5AzadC 12hpf totalRNA Rep2; Danio rerio; RNA Seq", "GSM5909697 r1", "GSM5909697", "1", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP360814", null, "loader:fastq load.py", "H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep2_Clean_Data1.fq.gz H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep2_Clean_Data2.fq.gz", "fastq fastq", 8417838534.0, 30315023.0, "GSM5909697 r1", "0:138.87 1:138.81", "A:1056052986;C:3111397305;G:3219318758;T:1030963544;N:105941", 138, 138, null, null, 1056052986, 3111397305, 3219318758, 1030963544, 105941, "SRX14241862", "SRS12062496", "SRA1376914", "Biomedical Genetics, University of Rochester Medical Center", "Biomedical Genetics, University of Rochester Medical Center", 2, 0.97654, 0.98322, 0.05557, 0.05458, 0.88483, 0.88434, 0.95181, 0.95236, 142, 142, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-21", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68646, "SRR18090808", "SRX14241861", "SRS12062495", "SRP360814", "PRJNA809026", "Competition for H2A.Z underlies the developmental impacts of repetitive element de repression", "GSE197131", "Transcriptome Analysis", "The histone variant H2A.Z is central to early embryonic development  determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "H2A.ZmCherry 5AzadC 12hpf totalRNA Rep1", "GSM5909696", null, "tissue:zebrafish embryos|developmental stage:12hpf overexpression|treatment:5AzadC|geo loc name:missing|collection date:missing", "H2A.ZmCherry 5AzadC 12hpf totalRNA Rep1", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. Differentially expressed genes were identified using DESeq2 v1.22.2 in R/3.5.1 Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters:   normalizeUsing RPKM   binSize 10 Genome build: Zv11 Supplementary files format and content: bigWig files and txt files", "zebrafish embryos", "Newly fertilized eggs were collected immediately post spawning  and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza dC   or with 0.1% DMSO for control group.", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", "Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle", "developmental stage:12hpf overexpression|treatment:5AzadC", "GSM5909696", "GSM5909696: H2A.ZmCherry 5AzadC 12hpf totalRNA Rep1; Danio rerio; RNA Seq", "GSM5909696 r1", "GSM5909696", "1", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP360814", null, "loader:fastq load.py", "H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep1_Clean_Data1.fq.gz H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep1_Clean_Data2.fq.gz", "fastq fastq", 8459255944.0, 30459385.0, "GSM5909696 r1", "0:138.89 1:138.83", "A:1038042916;C:3148721594;G:3268417368;T:1003964455;N:109611", 138, 138, null, null, 1038042916, 3148721594, 3268417368, 1003964455, 109611, "SRX14241861", "SRS12062495", "SRA1376914", "Biomedical Genetics, University of Rochester Medical Center", "Biomedical Genetics, University of Rochester Medical Center", 2, 0.9788, 0.98316, 0.05405, 0.05374, 0.90149, 0.9012, 0.96091, 0.96182, 142, 95, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-21", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68647, "SRR18090809", "SRX14241860", "SRS12062494", "SRP360814", "PRJNA809026", "Competition for H2A.Z underlies the developmental impacts of repetitive element de repression", "GSE197131", "Transcriptome Analysis", "The histone variant H2A.Z is central to early embryonic development  determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "H2A.ZmCherry DMSO 12hpf totalRNA Rep3", "GSM5909695", null, "tissue:zebrafish embryos|developmental stage:12hpf overexpression|treatment:DMSO|geo loc name:missing|collection date:missing", "H2A.ZmCherry DMSO 12hpf totalRNA Rep3", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. Differentially expressed genes were identified using DESeq2 v1.22.2 in R/3.5.1 Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters:   normalizeUsing RPKM   binSize 10 Genome build: Zv11 Supplementary files format and content: bigWig files and txt files", "zebrafish embryos", "Newly fertilized eggs were collected immediately post spawning  and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza dC   or with 0.1% DMSO for control group.", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", "Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle", "developmental stage:12hpf overexpression|treatment:DMSO", "GSM5909695", "GSM5909695: H2A.ZmCherry DMSO 12hpf totalRNA Rep3; Danio rerio; RNA Seq", "GSM5909695 r1", "GSM5909695", "1", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP360814", null, "loader:fastq load.py", "H2A.ZmCherry_DMSO_12hpf_totalRNA_Rep3_Clean_Data1.fq.gz H2A.ZmCherry_DMSO_12hpf_totalRNA_Rep3_Clean_Data2.fq.gz", "fastq fastq", 8361728983.0, 30085560.0, "GSM5909695 r1", "0:138.99 1:138.95", "A:1021320956;C:3113998482;G:3243440042;T:982860290;N:109213", 138, 138, null, null, 1021320956, 3113998482, 3243440042, 982860290, 109213, "SRX14241860", "SRS12062494", "SRA1376914", "Biomedical Genetics, University of Rochester Medical Center", "Biomedical Genetics, University of Rochester Medical Center", 2, 0.9776, 0.98258, 0.05657, 0.05665, 0.90611, 0.90552, 0.90822, 0.96352, 142, 142, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-21", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68648, "SRR18090810", "SRX14241859", "SRS12062493", "SRP360814", "PRJNA809026", "Competition for H2A.Z underlies the developmental impacts of repetitive element de repression", "GSE197131", "Transcriptome Analysis", "The histone variant H2A.Z is central to early embryonic development  determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "H2A.ZmCherry DMSO 12hpf totalRNA Rep2", "GSM5909694", null, "tissue:zebrafish embryos|developmental stage:12hpf overexpression|treatment:DMSO|geo loc name:missing|collection date:missing", "H2A.ZmCherry DMSO 12hpf totalRNA Rep2", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. 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In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "H2A.ZmCherry DMSO 12hpf totalRNA Rep1", "GSM5909693", null, "tissue:zebrafish embryos|developmental stage:12hpf overexpression|treatment:DMSO|geo loc name:missing|collection date:missing", "H2A.ZmCherry DMSO 12hpf totalRNA Rep1", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. 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In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "WT 5AzadC 12hpf totalRNA Rep3", "GSM5909692", null, "tissue:zebrafish embryos|developmental stage:12hpf type|treatment:5AzadC|geo loc name:missing|collection date:missing", "WT 5AzadC 12hpf totalRNA Rep3", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. 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