{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Blastula\" and technology = \"bulk\"", "rows": [[25275, "SRR25764093", "SRX21486761", "SRS18719061", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf RNA seq rep2", "GSM7734766", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT sphere 4 hpf RNA seq rep2", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings  retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters:   outSAMtype BAM SortedByCoordinate   outFilterMultimapNmax 1   outFilterMismatchNmax 1   quantMode TranscriptomeSAM GeneCounts   alignEndsType Local   seedSearchStartLmax 14   alignIntronMax 10000   outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research  #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT", "GSM7734766", "GSM7734766: WT sphere 4 hpf RNA seq rep2; Danio rerio; RNA Seq", "GSM7734766 r1", "GSM7734766", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research  #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_sphere_2.fastq.gz", "fastq", 2455317157.0, 30934591.0, "GSM7734766 r1", "0:79.37", "A:614860604;C:588586084;G:522132289;T:729655621;N:82559", 79, null, null, null, 614860604, 588586084, 522132289, 729655621, 82559, "SRX21486761", "SRS18719061", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.94124, null, 0.10502, null, 0.74876, null, 0.57752, null, 80, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [25276, "SRR25764094", "SRX21486760", "SRS18719060", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf RNA seq rep1", "GSM7734765", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT sphere 4 hpf RNA seq rep1", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings  retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters:   outSAMtype BAM SortedByCoordinate   outFilterMultimapNmax 1   outFilterMismatchNmax 1   quantMode TranscriptomeSAM GeneCounts   alignEndsType Local   seedSearchStartLmax 14   alignIntronMax 10000   outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research  #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT", "GSM7734765", "GSM7734765: WT sphere 4 hpf RNA seq rep1; Danio rerio; RNA Seq", "GSM7734765 r1", "GSM7734765", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research  #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_sphere_1.fastq.gz", "fastq", 2399640874.0, 30232118.0, "GSM7734765 r1", "0:79.37", "A:589069860;C:593745131;G:511439690;T:705305674;N:80519", 79, null, null, null, 589069860, 593745131, 511439690, 705305674, 80519, "SRX21486760", "SRS18719060", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.85882, null, 0.11848, null, 0.75122, null, 0.5883, null, 80, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30050, "SRR27730713", "SRX23396345", "SRS20257259", "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 /  4 hpf embryo", "zebrafish embryo hamp /  4hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:4 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: 4hpf embryo", "W 24", "W 24", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp4h-3_2.fq.gz hamp4h-3_1.fq.gz", "fastq fastq", 6261088500.0, 20870295.0, "hamp4h 3 1.fq.gz", "0:150 1:150", "A:1668720393;C:1449635670;G:1495531397;T:1647100279;N:100761", 150, 150, null, null, 1668720393, 1449635670, 1495531397, 1647100279, 100761, "SRX23396345", "SRS20257259", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94424, 0.94159, 0.04146, 0.0415, 0.75089, 0.75201, 0.48393, 0.48457, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30061, "SRR27730724", "SRX23396334", "SRS20257248", "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 /  4 hpf embryo", "zebrafish embryo hamp /  4hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:4 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: 4hpf embryo", "W 23", "W 23", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp4h-2_1.fq.gz hamp4h-2_2.fq.gz", "fastq fastq", 6140359800.0, 20467866.0, "hamp4h 2 1.fq.gz", "0:150 1:150", "A:1622433757;C:1437175847;G:1481587196;T:1599071088;N:91912", 150, 150, null, null, 1622433757, 1437175847, 1481587196, 1599071088, 91912, "SRX23396334", "SRS20257248", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94763, 0.94713, 0.03975, 0.03948, 0.75045, 0.75193, 0.48915, 0.48855, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30062, "SRR27730725", "SRX23396333", "SRS20257247", "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 /  4 hpf embryo", "zebrafish embryo hamp /  4hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:4 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: 4hpf embryo", "W 22", "W 22", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp4h-1_1.fq.gz hamp4h-1_2.fq.gz", "fastq fastq", 6482302500.0, 21607675.0, "hamp4h 1 1.fq.gz", "0:150 1:150", "A:1723398342;C:1504238189;G:1551942847;T:1702630056;N:93066", 150, 150, null, null, 1723398342, 1504238189, 1551942847, 1702630056, 93066, "SRX23396333", "SRS20257247", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94434, 0.94083, 0.04297, 0.04235, 0.75327, 0.75526, 0.48487, 0.4837, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30063, "SRR27674233", "SRX23341580", "SRS20203706", "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 4 phf embryo", "zebrafish embryo 4 phf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:4 phf|dev stage:4 phf|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: 4hpf embryo", "W 3", "W 3", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT4h-3_1.fq.gz WT4h-3_2.fq.gz", "fastq fastq", 5799593100.0, 19331977.0, "WT4h 3 1.fq.gz", "0:150 1:150", "A:1543677690;C:1345529657;G:1387996505;T:1522341224;N:48024", 150, 150, null, null, 1543677690, 1345529657, 1387996505, 1522341224, 48024, "SRX23341580", "SRS20203706", "SRA1789158", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94823, 0.94693, 0.0386, 0.03884, 0.74686, 0.74769, 0.47863, 0.48203, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-22", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30064, "SRR27674234", "SRX23341579", "SRS20203705", "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 4 phf embryo", "zebrafish embryo 4 phf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:4 phf|dev stage:4 phf|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: 4hpf embryo", "W 2", "W 2", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT4h-2_1.fq.gz WT4h-2_2.fq.gz", "fastq fastq", 6408374700.0, 21361249.0, "WT4h 2 1.fq.gz", "0:150 1:150", "A:1700326501;C:1489928909;G:1544130015;T:1673936668;N:52607", 150, 150, null, null, 1700326501, 1489928909, 1544130015, 1673936668, 52607, "SRX23341579", "SRS20203705", "SRA1789158", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94833, 0.94724, 0.03589, 0.03528, 0.74521, 0.74665, 0.47991, 0.47552, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-22", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30065, "SRR27674235", "SRX23341578", "SRS20203704", "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 4 phf embryo", "zebrafish embryo 4 phf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:4 phf|dev stage:4 phf|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: 4hpf embryo", "W 1", "W 1", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT4h-1_1.fq.gz WT4h-1_2.fq.gz", "fastq fastq", 6176335500.0, 20587785.0, "WT4h 1 1.fq.gz", "0:150 1:150", "A:1639564255;C:1436792246;G:1481775020;T:1618153065;N:50914", 150, 150, null, null, 1639564255, 1436792246, 1481775020, 1618153065, 50914, "SRX23341578", "SRS20203704", "SRA1789158", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94837, 0.94497, 0.03675, 0.03629, 0.74393, 0.74497, 0.48332, 0.48392, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-22", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30749, "SRR30167500", "SRX25634206", "SRS22278604", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "pCas13d al1  4hpf  rep3", "GSM8446429", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "pCas13d al1  4hpf  rep3", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8446429", "GSM8446429: pCas13d al1  4hpf  rep3; Danio rerio; RNA Seq", "GSM8446429 r1", "GSM8446429", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "L67855_S11_L001_R1_001.fastq.gz L67855_S11_L001_R2_001.fastq.gz", "fastq fastq", 2565767500.0, 25657675.0, "GSM8446429 r1", "0:50 1:50", "A:676771006;C:596998503;G:603560859;T:688437132;N:0", 50, 50, null, null, 676771006, 596998503, 603560859, 688437132, 0, "SRX25634206", "SRS22278604", "SRA1942483", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-08-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30750, "SRR30167501", "SRX25634205", "SRS22278605", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "pCas13d al1  4hpf  rep2", "GSM8446428", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "pCas13d al1  4hpf  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8446428", "GSM8446428: pCas13d al1  4hpf  rep2; Danio rerio; RNA Seq", "GSM8446428 r1", "GSM8446428", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "L67854_S10_L001_R1_001.fastq.gz L67854_S10_L001_R2_001.fastq.gz", "fastq fastq", 2528276500.0, 25282765.0, "GSM8446428 r1", "0:50 1:50", "A:664250318;C:589008342;G:598067975;T:676949865;N:0", 50, 50, null, null, 664250318, 589008342, 598067975, 676949865, 0, "SRX25634205", "SRS22278605", "SRA1942483", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-08-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30751, "SRR30167502", "SRX25634204", "SRS22278602", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "pCas13d al1  4hpf  rep1", "GSM8446427", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "pCas13d al1  4hpf  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8446427", "GSM8446427: pCas13d al1  4hpf  rep1; Danio rerio; RNA Seq", "GSM8446427 r1", "GSM8446427", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "L67853_S9_L001_R1_001.fastq.gz L67853_S9_L001_R2_001.fastq.gz", "fastq fastq", 2416897800.0, 24168978.0, "GSM8446427 r1", "0:50 1:50", "A:636467903;C:563622671;G:568978039;T:647829187;N:0", 50, 50, null, null, 636467903, 563622671, 568978039, 647829187, 0, "SRX25634204", "SRS22278602", "SRA1942483", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-08-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30752, "SRR30167503", "SRX25634203", "SRS22278601", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "znf281b KD  4hpf  rep3", "GSM8446426", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "znf281b KD  4hpf  rep3", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8446426", "GSM8446426: znf281b KD  4hpf  rep3; Danio rerio; RNA Seq", "GSM8446426 r1", "GSM8446426", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "L67851_S7_L001_R1_001.fastq.gz L67851_S7_L001_R2_001.fastq.gz", "fastq fastq", 2366597500.0, 23665975.0, "GSM8446426 r1", "0:50 1:50", "A:620883932;C:547989723;G:563335901;T:634387944;N:0", 50, 50, null, null, 620883932, 547989723, 563335901, 634387944, 0, "SRX25634203", "SRS22278601", "SRA1942483", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-08-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30753, "SRR30167504", "SRX25634202", "SRS22278600", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "znf281b KD  4hpf  rep2", "GSM8446425", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "znf281b KD  4hpf  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8446425", "GSM8446425: znf281b KD  4hpf  rep2; Danio rerio; RNA Seq", "GSM8446425 r1", "GSM8446425", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "L67850_S6_L001_R1_001.fastq.gz L67850_S6_L001_R2_001.fastq.gz", "fastq fastq", 2497293900.0, 24972939.0, "GSM8446425 r1", "0:50 1:50", "A:657452880;C:579618079;G:589789328;T:670433613;N:0", 50, 50, null, null, 657452880, 579618079, 589789328, 670433613, 0, "SRX25634202", "SRS22278600", "SRA1942483", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-08-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30754, "SRR30167505", "SRX25634201", "SRS22278596", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "znf281b KD  4hpf  rep1", "GSM8446424", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "znf281b KD  4hpf  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8446424", "GSM8446424: znf281b KD  4hpf  rep1; Danio rerio; RNA Seq", "GSM8446424 r1", "GSM8446424", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit  following the \u201cAdapting Libraries for the G4 \u2013 Retaining Original Indices\u201d protocol. The converted pool was sequenced on an F2 flow cell Cat. No. 700104 on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit Cat. No. 700141  using Instrument Control Software G4 23.08.1 1 with the following read length: 8 bp Index1  50 bp Read1  and 8 bp Index2  50 bp Read 2. Following sequencing  sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "L67849_S5_L001_R1_001.fastq.gz L67849_S5_L001_R2_001.fastq.gz", "fastq fastq", 2607154500.0, 26071545.0, "GSM8446424 r1", "0:50 1:50", "A:685092511;C:605305852;G:618493032;T:698263105;N:0", 50, 50, null, null, 685092511, 605305852, 618493032, 698263105, 0, "SRX25634201", "SRS22278596", "SRA1942483", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-08-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30766, "SRR28348932", "SRX23954964", "SRS20755385", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo  4hpf  rep3", "GSM8147861", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo  4hpf  rep3", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8147861", "GSM8147861: Zebrafish Embryo  4hpf  rep3; Danio rerio; RNA Seq", "GSM8147861 r1", "GSM8147861", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_4hpf_3.fastq", "fastq", 1795835160.0, 23629410.0, "GSM8147861 r1", "0:76", "A:438577940;C:442051089;G:414188325;T:500933940;N:83866", 76, null, null, null, 438577940, 442051089, 414188325, 500933940, 83866, "SRX23954964", "SRS20755385", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30767, "SRR28348933", "SRX23954963", "SRS20755384", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo  4hpf  rep2", "GSM8147860", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo  4hpf  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8147860", "GSM8147860: Zebrafish Embryo  4hpf  rep2; Danio rerio; RNA Seq", "GSM8147860 r1", "GSM8147860", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_4hpf_2.fastq", "fastq", 1665073892.0, 21908867.0, "GSM8147860 r1", "0:76", "A:405272447;C:411954373;G:384597098;T:463177801;N:72173", 76, null, null, null, 405272447, 411954373, 384597098, 463177801, 72173, "SRX23954963", "SRS20755384", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30768, "SRR28348934", "SRX23954962", "SRS20755383", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo  4hpf  rep1", "GSM8147859", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo  4hpf  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:4hpf|genotype:AB  TF and TLF", "GSM8147859", "GSM8147859: Zebrafish Embryo  4hpf  rep1; Danio rerio; RNA Seq", "GSM8147859 r1", "GSM8147859", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_4hpf_1.fastq", "fastq", 1494269972.0, 19661447.0, "GSM8147859 r1", "0:76", "A:365052201;C:369717962;G:351357642;T:408073055;N:69112", 76, null, null, null, 365052201, 369717962, 351357642, 408073055, 69112, "SRX23954962", "SRS20755383", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34032, "SRR31033342", "SRX26418811", "SRS22938447", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  Riboseq  M sphere 5", "GSM8579734", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  M sphere 5", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a", "GSM8579734", "GSM8579734: Zebrafish  Riboseq  M sphere 5; Danio rerio; RNA Seq", "GSM8579734 r1", "GSM8579734", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "M-sphere-5_L1_1.fq.gz M-sphere-5_L1_2.fq.gz", "fastq fastq", 6386202900.0, 21287343.0, "GSM8579734 r1", "0:150 1:150", "A:1749323046;C:1447024706;G:1497348312;T:1692462495;N:44341", 150, 150, null, null, 1749323046, 1447024706, 1497348312, 1692462495, 44341, "SRX26418811", "SRS22938447", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34033, "SRR31033343", "SRX26418810", "SRS22938444", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  Riboseq  M sphere 4", "GSM8579733", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  M sphere 4", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a", "GSM8579733", "GSM8579733: Zebrafish  Riboseq  M sphere 4; Danio rerio; RNA Seq", "GSM8579733 r1", "GSM8579733", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "M-sphere-4_L1_1.fq.gz M-sphere-4_L1_2.fq.gz", "fastq fastq", 7329708000.0, 24432360.0, "GSM8579733 r1", "0:150 1:150", "A:1999459748;C:1667498786;G:1726069847;T:1936629080;N:50539", 150, 150, null, null, 1999459748, 1667498786, 1726069847, 1936629080, 50539, "SRX26418810", "SRS22938444", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34034, "SRR31033344", "SRX26418809", "SRS22938445", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  Riboseq  M sphere 2", "GSM8579732", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  M sphere 2", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a", "GSM8579732", "GSM8579732: Zebrafish  Riboseq  M sphere 2; Danio rerio; RNA Seq", "GSM8579732 r1", "GSM8579732", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "M-sphere-2_L1_1.fq.gz M-sphere-2_L1_2.fq.gz", "fastq fastq", 6614502300.0, 22048341.0, "GSM8579732 r1", "0:150 1:150", "A:1811784017;C:1496173021;G:1549885996;T:1756614738;N:44528", 150, 150, null, null, 1811784017, 1496173021, 1549885996, 1756614738, 44528, "SRX26418809", "SRS22938445", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34035, "SRR31033352", "SRX26418808", "SRS22938439", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  Riboseq  M sphere 1", "GSM8579731", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  M sphere 1", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a", "GSM8579731", "GSM8579731: Zebrafish  Riboseq  M sphere 1; Danio rerio; RNA Seq", "GSM8579731 r1", "GSM8579731", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "M-sphere-1_L1_1.fq.gz M-sphere-1_L1_2.fq.gz", "fastq fastq", 7080587100.0, 23601957.0, "GSM8579731 r1", "0:150 1:150", "A:1946013215;C:1594400814;G:1652448966;T:1887676214;N:47891", 150, 150, null, null, 1946013215, 1594400814, 1652448966, 1887676214, 47891, "SRX26418808", "SRS22938439", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34044, "SRR31033360", "SRX26418799", "SRS22938436", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  RNAseq  Sibling sphere 4", "GSM8579722", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing", "Zebrafish  RNAseq  Sibling sphere 4", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type", "GSM8579722", "GSM8579722: Zebrafish  RNAseq  Sibling sphere 4; Danio rerio; RNA Seq", "GSM8579722 r1", "GSM8579722", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "Sibling-sphere-4_L1_1.fq.gz Sibling-sphere-4_L1_2.fq.gz", "fastq fastq", 7056333000.0, 23521110.0, "GSM8579722 r1", "0:150 1:150", "A:1940035016;C:1589047995;G:1648953235;T:1878249310;N:47444", 150, 150, null, null, 1940035016, 1589047995, 1648953235, 1878249310, 47444, "SRX26418799", "SRS22938436", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34045, "SRR31033354", "SRX26418798", "SRS22938429", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  RNAseq  Sibling sphere 3", "GSM8579721", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing", "Zebrafish  RNAseq  Sibling sphere 3", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type", "GSM8579721", "GSM8579721: Zebrafish  RNAseq  Sibling sphere 3; Danio rerio; RNA Seq", "GSM8579721 r1", "GSM8579721", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "Sibling-sphere-3_L1_1.fq.gz Sibling-sphere-3_L1_2.fq.gz", "fastq fastq", 7102058100.0, 23673527.0, "GSM8579721 r1", "0:150 1:150", "A:1932660580;C:1619713195;G:1685329939;T:1864306893;N:47493", 150, 150, null, null, 1932660580, 1619713195, 1685329939, 1864306893, 47493, "SRX26418798", "SRS22938429", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34046, "SRR31033359", "SRX26418797", "SRS22938433", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  RNAseq  Sibling sphere 1", "GSM8579720", null, "source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing", "Zebrafish  RNAseq  Sibling sphere 1", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type", "GSM8579720", "GSM8579720: Zebrafish  RNAseq  Sibling sphere 1; Danio rerio; RNA Seq", "GSM8579720 r1", "GSM8579720", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "Sibling-sphere-1_L1_1.fq.gz Sibling-sphere-1_L1_2.fq.gz", "fastq fastq", 6375563100.0, 21251877.0, "GSM8579720 r1", "0:150 1:150", "A:1748656292;C:1440631635;G:1494630558;T:1691601145;N:43470", 150, 150, null, null, 1748656292, 1440631635, 1494630558, 1691601145, 43470, "SRX26418797", "SRS22938433", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34364, "SRR31695142", "SRX27056958", "SRS23518718", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep4", "GSM8678154", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep4", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678154", "GSM8678154: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep4; Danio rerio; RNA Seq", "GSM8678154 r1", "GSM8678154", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep4_R1.fastq.gz T_pRfxCas13d_g1Syn_rep4_R2.fastq.gz", "fastq fastq", 1869396000.0, 12462640.0, "GSM8678154 r1", "0:75 1:75", "A:497545631;C:434254877;G:436435676;T:501090064;N:69752", 75, 75, null, null, 497545631, 434254877, 436435676, 501090064, 69752, "SRX27056958", "SRS23518718", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34365, "SRR31695143", "SRX27056957", "SRS23518717", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep3", "GSM8678153", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep3", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678153", "GSM8678153: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep3; Danio rerio; RNA Seq", "GSM8678153 r1", "GSM8678153", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep3_R1.fastq.gz T_pRfxCas13d_g1Syn_rep3_R2.fastq.gz", "fastq fastq", 1939758450.0, 12931723.0, "GSM8678153 r1", "0:75 1:75", "A:510928336;C:455303431;G:458245636;T:515206838;N:74209", 75, 75, null, null, 510928336, 455303431, 458245636, 515206838, 74209, "SRX27056957", "SRS23518717", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34366, "SRR31695144", "SRX27056956", "SRS23518716", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep4", "GSM8678152", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep4", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678152", "GSM8678152: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep4; Danio rerio; RNA Seq", "GSM8678152 r1", "GSM8678152", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep4_R1.fastq.gz T_pRfxCas13d_g3Syn_rep4_R2.fastq.gz", "fastq fastq", 1372458150.0, 9149721.0, "GSM8678152 r1", "0:75 1:75", "A:363668106;C:319963774;G:322725620;T:366049498;N:51152", 75, 75, null, null, 363668106, 319963774, 322725620, 366049498, 51152, "SRX27056956", "SRS23518716", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34367, "SRR31695145", "SRX27056955", "SRS23518715", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep3", "GSM8678151", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep3", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678151", "GSM8678151: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep3; Danio rerio; RNA Seq", "GSM8678151 r1", "GSM8678151", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep3_R1.fastq.gz T_pRfxCas13d_g3Syn_rep3_R2.fastq.gz", "fastq fastq", 1716718500.0, 11444790.0, "GSM8678151 r1", "0:75 1:75", "A:454308432;C:401470287;G:402968652;T:457908108;N:63021", 75, 75, null, null, 454308432, 401470287, 402968652, 457908108, 63021, "SRX27056955", "SRS23518715", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34368, "SRR31695150", "SRX27056954", "SRS23518714", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control  rep6", "GSM8678150", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control  rep6", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678150", "GSM8678150: RfxCas13d control  rep6; Danio rerio; RNA Seq", "GSM8678150 r1", "GSM8678150", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep6_R1.fastq.gz T_pRfxCas13d_rep6_R2.fastq.gz", "fastq fastq", 1820554200.0, 12137028.0, "GSM8678150 r1", "0:75 1:75", "A:480817156;C:426951021;G:428763810;T:483952927;N:69286", 75, 75, null, null, 480817156, 426951021, 428763810, 483952927, 69286, "SRX27056954", "SRS23518714", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34369, "SRR31695146", "SRX27056953", "SRS23518713", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep2", "GSM8678149", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep2", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678149", "GSM8678149: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep2; Danio rerio; RNA Seq", "GSM8678149 r1", "GSM8678149", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep2_R1.fastq.gz T_pRfxCas13d_g1Syn_rep2_R2.fastq.gz", "fastq fastq", 1686506550.0, 11243377.0, "GSM8678149 r1", "0:75 1:75", "A:445306390;C:395515087;G:396951869;T:448671449;N:61755", 75, 75, null, null, 445306390, 395515087, 396951869, 448671449, 61755, "SRX27056953", "SRS23518713", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34370, "SRR31695147", "SRX27056952", "SRS23518712", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep1", "GSM8678148", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep1", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678148", "GSM8678148: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4  rep1; Danio rerio; RNA Seq", "GSM8678148 r1", "GSM8678148", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep1_R1.fastq.gz T_pRfxCas13d_g1Syn_rep1_R2.fastq.gz", "fastq fastq", 2099239050.0, 13994927.0, "GSM8678148 r1", "0:75 1:75", "A:555464950;C:490168575;G:492715156;T:560811934;N:78435", 75, 75, null, null, 555464950, 490168575, 492715156, 560811934, 78435, "SRX27056952", "SRS23518712", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34371, "SRR31695148", "SRX27056951", "SRS23518711", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep2", "GSM8678147", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep2", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678147", "GSM8678147: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep2; Danio rerio; RNA Seq", "GSM8678147 r1", "GSM8678147", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep2_R1.fastq.gz T_pRfxCas13d_g3Syn_rep2_R2.fastq.gz", "fastq fastq", 1855616550.0, 12370777.0, "GSM8678147 r1", "0:75 1:75", "A:490735862;C:434070234;G:436325424;T:494415408;N:69622", 75, 75, null, null, 490735862, 434070234, 436325424, 494415408, 69622, "SRX27056951", "SRS23518711", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34372, "SRR31695149", "SRX27056950", "SRS23518710", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep1", "GSM8678146", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep1", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   Chemically Synthesized gRNA", "GSM8678146", "GSM8678146: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4  rep1; Danio rerio; RNA Seq", "GSM8678146 r1", "GSM8678146", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep1_R1.fastq.gz T_pRfxCas13d_g3Syn_rep1_R2.fastq.gz", "fastq fastq", 2029890750.0, 13532605.0, "GSM8678146 r1", "0:75 1:75", "A:536398630;C:474872197;G:478734292;T:539809587;N:76044", 75, 75, null, null, 536398630, 474872197, 478734292, 539809587, 76044, "SRX27056950", "SRS23518710", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34373, "SRR31695155", "SRX27056949", "SRS23518709", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control  rep5", "GSM8678145", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control  rep5", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678145", "GSM8678145: RfxCas13d control  rep5; Danio rerio; RNA Seq", "GSM8678145 r1", "GSM8678145", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep5_R1.fastq.gz T_pRfxCas13d_rep5_R2.fastq.gz", "fastq fastq", 1699800000.0, 11332000.0, "GSM8678145 r1", "0:75 1:75", "A:448834438;C:398037498;G:400242751;T:452619971;N:65342", 75, 75, null, null, 448834438, 398037498, 400242751, 452619971, 65342, "SRX27056949", "SRS23518709", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34374, "SRR31695151", "SRX27056948", "SRS23518708", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep3", "GSM8678144", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep3", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678144", "GSM8678144: RfxCas13d + g3 IVTed si:dkey 93m18.4  rep3; Danio rerio; RNA Seq", "GSM8678144 r1", "GSM8678144", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3_rep3_R1.fastq.gz T_pRfxCas13d_g3_rep3_R2.fastq.gz", "fastq fastq", 1603289100.0, 10688594.0, "GSM8678144 r1", "0:75 1:75", "A:420349766;C:379529179;G:379756700;T:423592677;N:60778", 75, 75, null, null, 420349766, 379529179, 379756700, 423592677, 60778, "SRX27056948", "SRS23518708", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34375, "SRR31695154", "SRX27056947", "SRS23518706", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep2", "GSM8678143", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep2", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678143", "GSM8678143: RfxCas13d + g3 IVTed si:dkey 93m18.4  rep2; Danio rerio; RNA Seq", "GSM8678143 r1", "GSM8678143", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3_rep2_R1.fastq.gz T_pRfxCas13d_g3_rep2_R2.fastq.gz", "fastq fastq", 1700840400.0, 11338936.0, "GSM8678143 r1", "0:75 1:75", "A:447219410;C:401375108;G:401866426;T:450317233;N:62223", 75, 75, null, null, 447219410, 401375108, 401866426, 450317233, 62223, "SRX27056947", "SRS23518706", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34376, "SRR31695152", "SRX27056946", "SRS23518707", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control  rep4", "GSM8678142", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control  rep4", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678142", "GSM8678142: RfxCas13d control  rep4; Danio rerio; RNA Seq", "GSM8678142 r1", "GSM8678142", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep4_R1.fastq.gz T_pRfxCas13d_rep4_R2.fastq.gz", "fastq fastq", 1390819050.0, 9272127.0, "GSM8678142 r1", "0:75 1:75", "A:365774543;C:327280225;G:328329658;T:369385513;N:49111", 75, 75, null, null, 365774543, 327280225, 328329658, 369385513, 49111, "SRX27056946", "SRS23518707", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34377, "SRR31695153", "SRX27056945", "SRS23518705", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep1", "GSM8678141", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep1", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678141", "GSM8678141: RfxCas13d + g3 IVTed si:dkey 93m18.4  rep1; Danio rerio; RNA Seq", "GSM8678141 r1", "GSM8678141", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3_rep1_R1.fastq.gz T_pRfxCas13d_g3_rep1_R2.fastq.gz", "fastq fastq", 1979083650.0, 13193891.0, "GSM8678141 r1", "0:75 1:75", "A:521444446;C:467332323;G:468450230;T:521779923;N:76728", 75, 75, null, null, 521444446, 467332323, 468450230, 521779923, 76728, "SRX27056945", "SRS23518705", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34378, "SRR31695156", "SRX27056944", "SRS23518704", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control  rep3", "GSM8678140", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control  rep3", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678140", "GSM8678140: RfxCas13d control  rep3; Danio rerio; RNA Seq", "GSM8678140 r1", "GSM8678140", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep3_R1.fastq.gz T_pRfxCas13d_rep3_R2.fastq.gz", "fastq fastq", 1520356800.0, 10135712.0, "GSM8678140 r1", "0:75 1:75", "A:400447283;C:357034714;G:358393387;T:404426537;N:54879", 75, 75, null, null, 400447283, 357034714, 358393387, 404426537, 54879, "SRX27056944", "SRS23518704", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34379, "SRR31695157", "SRX27056943", "SRS23518703", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 IVTed si:dkey 93m18.4  rep3", "GSM8678139", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 IVTed si:dkey 93m18.4  rep3", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678139", "GSM8678139: RfxCas13d + g1 IVTed si:dkey 93m18.4  rep3; Danio rerio; RNA Seq", "GSM8678139 r1", "GSM8678139", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1_rep3_R1.fastq.gz T_pRfxCas13d_g1_rep3_R2.fastq.gz", "fastq fastq", 1890203250.0, 12601355.0, "GSM8678139 r1", "0:75 1:75", "A:501821472;C:441868721;G:441485425;T:504956362;N:71270", 75, 75, null, null, 501821472, 441868721, 441485425, 504956362, 71270, "SRX27056943", "SRS23518703", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34380, "SRR31695162", "SRX27056942", "SRS23518702", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g2 IVTed si:dkey 93m18.4  rep3", "GSM8678138", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g2 IVTed si:dkey 93m18.4  rep3", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678138", "GSM8678138: RfxCas13d + g2 IVTed si:dkey 93m18.4  rep3; Danio rerio; RNA Seq", "GSM8678138 r1", "GSM8678138", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g2_rep3_R1.fastq.gz T_pRfxCas13d_g2_rep3_R2.fastq.gz", "fastq fastq", 1839509400.0, 12263396.0, "GSM8678138 r1", "0:75 1:75", "A:485779725;C:432231942;G:432933832;T:488492257;N:71644", 75, 75, null, null, 485779725, 432231942, 432933832, 488492257, 71644, "SRX27056942", "SRS23518702", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34381, "SRR31695158", "SRX27056941", "SRS23518701", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 IVTed si:dkey 93m18.4  rep2", "GSM8678137", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 IVTed si:dkey 93m18.4  rep2", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678137", "GSM8678137: RfxCas13d + g1 IVTed si:dkey 93m18.4  rep2; Danio rerio; RNA Seq", "GSM8678137 r1", "GSM8678137", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1_rep2_R1.fastq.gz T_pRfxCas13d_g1_rep2_R2.fastq.gz", "fastq fastq", 1742339250.0, 11615595.0, "GSM8678137 r1", "0:75 1:75", "A:461346904;C:406656276;G:409937021;T:464333259;N:65790", 75, 75, null, null, 461346904, 406656276, 409937021, 464333259, 65790, "SRX27056941", "SRS23518701", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34382, "SRR31695161", "SRX27056940", "SRS23518700", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control  rep2", "GSM8678136", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control  rep2", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678136", "GSM8678136: RfxCas13d control  rep2; Danio rerio; RNA Seq", "GSM8678136 r1", "GSM8678136", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep2_R1.fastq.gz T_pRfxCas13d_rep2_R2.fastq.gz", "fastq fastq", 1800739800.0, 12004932.0, "GSM8678136 r1", "0:75 1:75", "A:477337887;C:421087001;G:421493244;T:480753457;N:68211", 75, 75, null, null, 477337887, 421087001, 421493244, 480753457, 68211, "SRX27056940", "SRS23518700", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34383, "SRR31695159", "SRX27056939", "SRS23518699", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g2 IVTed si:dkey 93m18.4  rep2", "GSM8678135", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g2 IVTed si:dkey 93m18.4  rep2", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678135", "GSM8678135: RfxCas13d + g2 IVTed si:dkey 93m18.4  rep2; Danio rerio; RNA Seq", "GSM8678135 r1", "GSM8678135", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g2_rep2_R1.fastq.gz T_pRfxCas13d_g2_rep2_R2.fastq.gz", "fastq fastq", 1752030300.0, 11680202.0, "GSM8678135 r1", "0:75 1:75", "A:462116558;C:411708555;G:412346341;T:465792629;N:66217", 75, 75, null, null, 462116558, 411708555, 412346341, 465792629, 66217, "SRX27056939", "SRS23518699", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34384, "SRR31695160", "SRX27056938", "SRS23518698", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 IVTed si:dkey 93m18.4  rep1", "GSM8678134", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 IVTed si:dkey 93m18.4  rep1", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678134", "GSM8678134: RfxCas13d + g1 IVTed si:dkey 93m18.4  rep1; Danio rerio; RNA Seq", "GSM8678134 r1", "GSM8678134", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1_rep1_R1.fastq.gz T_pRfxCas13d_g1_rep1_R2.fastq.gz", "fastq fastq", 1724105250.0, 11494035.0, "GSM8678134 r1", "0:75 1:75", "A:456793309;C:403294318;G:403256373;T:460696014;N:65236", 75, 75, null, null, 456793309, 403294318, 403256373, 460696014, 65236, "SRX27056938", "SRS23518698", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34385, "SRR31695163", "SRX27056937", "SRS23518697", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g2 IVTed si:dkey 93m18.4  rep1", "GSM8678133", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g2 IVTed si:dkey 93m18.4  rep1", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown   IVTed gRNA", "GSM8678133", "GSM8678133: RfxCas13d + g2 IVTed si:dkey 93m18.4  rep1; Danio rerio; RNA Seq", "GSM8678133 r1", "GSM8678133", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g2_rep1_R1.fastq.gz T_pRfxCas13d_g2_rep1_R2.fastq.gz", "fastq fastq", 1903402350.0, 12689349.0, "GSM8678133 r1", "0:75 1:75", "A:501904806;C:447043548;G:448270395;T:506113883;N:69718", 75, 75, null, null, 501904806, 447043548, 448270395, 506113883, 69718, "SRX27056937", "SRS23518697", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34386, "SRR31695164", "SRX27056936", "SRS23518696", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However  the efficiency of the system can be enhanced in vivo  and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here  we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos  by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown  an improved nuclear targeting  and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore  our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects  except for targeting extremely abundant RNAs. For that  we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether  these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control  rep1", "GSM8678132", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control  rep1", "Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678132", "GSM8678132: RfxCas13d control  rep1; Danio rerio; RNA Seq", "GSM8678132 r1", "GSM8678132", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA  as assessed using the Bioanalyzer Agilent  with the Watchmaker mRNA Library Prep Kit Watchmaker  Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification  2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter  Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup  and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen  Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled  quantified  and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep1_R1.fastq.gz T_pRfxCas13d_rep1_R2.fastq.gz", "fastq fastq", 1980525450.0, 13203503.0, "GSM8678132 r1", "0:75 1:75", "A:522445746;C:464027491;G:467474918;T:526505284;N:72011", 75, 75, null, null, 522445746, 464027491, 467474918, 526505284, 72011, "SRX27056936", "SRS23518696", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [38348, "SRR1785168", "SRX864139", "SRS834998", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "sphere cells rep1", "GSM1600044", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:sphere cells", "sphere cells rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:sphere cells", "GSM1600044", "GSM1600044: sphere cells rep1; Danio rerio; RNA Seq", "GSM1600044", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W10T_1.fastq.gz", "fastq", 9786365912.0, 96894712.0, "GSM1600044 r1", "0:101", "A:2573654910;C:2329556867;G:2311713480;T:2571211477;N:229178", 101, null, null, null, 2573654910, 2329556867, 2311713480, 2571211477, 229178, "SRX864139", "SRS834998", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95572, null, 0.05587, null, 0.73657, null, 0.48128, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38349, "SRR1785167", "SRX864138", "SRS834995", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "1000 cell rep1", "GSM1600043", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:1000 cells", "1000 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:1000 cells", "GSM1600043", "GSM1600043: 1000 cell rep1; Danio rerio; RNA Seq", "GSM1600043", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W9T_1.fastq.gz", "fastq", 8394219282.0, 83111082.0, "GSM1600043 r1", "0:101", "A:2195214424;C:2012486651;G:1991514912;T:2194810285;N:193010", 101, null, null, null, 2195214424, 2012486651, 1991514912, 2194810285, 193010, "SRX864138", "SRS834995", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95627, null, 0.02474, null, 0.75761, null, 0.47804, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38350, "SRR1785166", "SRX864137", "SRS834994", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "256 cell rep1", "GSM1600042", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:256 cell", "256 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:256 cell", "GSM1600042", "GSM1600042: 256 cell rep1; Danio rerio; RNA Seq", "GSM1600042", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600042", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W8T_1.fastq.gz", "fastq", 7155728901.0, 70848801.0, "GSM1600042 r1", "0:101", "A:1868886025;C:1718971317;G:1698634177;T:1869072256;N:165126", 101, null, null, null, 1868886025, 1718971317, 1698634177, 1869072256, 165126, "SRX864137", "SRS834994", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95828, null, 0.02188, null, 0.76307, null, 0.47861, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38351, "SRR1785165", "SRX864136", "SRS835002", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "128 cell rep1", "GSM1600041", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:128 cell", "128 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:128 cell", "GSM1600041", "GSM1600041: 128 cell rep1; Danio rerio; RNA Seq", "GSM1600041", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600041", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W7T_1.fastq.gz", "fastq", 11606209465.0, 114912965.0, "GSM1600041 r1", "0:101", "A:2959737203;C:2867533898;G:2855568487;T:2922947397;N:422480", 101, null, null, null, 2959737203, 2867533898, 2855568487, 2922947397, 422480, "SRX864136", "SRS835002", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95887, null, 0.01798, null, 0.76824, null, 0.47695, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [47617, "SRR6784691", "SRX3744229", "SRS3000697", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 5 hpf whole embryo injected with TUT47MO Exp. ID: rs2", "GSM3024083", null, "tissue:Zebrafish whole embryo|hpf translation blocking  TUT7 translation blocking|strain:AB", "Zebrafish 5 hpf whole embryo injected with TUT47MO Exp. ID: rs2", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking  TUT7 translation blocking|strain:AB", "GSM3024083", "GSM3024083: Zebrafish 5 hpf whole embryo injected with TUT47MO Exp. ID: rs2; Danio rerio; RNA Seq", "GSM3024083", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs2-TUT47MO-5hpf_R1.fastq.gz rs2-TUT47MO-5hpf_R2.fastq.gz", "fastq fastq", 5956989896.0, 39190723.0, "GSM3024083 r1", "0:76 1:76", "A:1416702080;C:1543800970;G:1539813949;T:1454939015;N:1733882", 76, 76, null, null, 1416702080, 1543800970, 1539813949, 1454939015, 1733882, "SRX3744229", "SRS3000697", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.9294, 0.93064, 0.16382, 0.16164, 0.75197, 0.7529, 0.6297, 0.62272, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47618, "SRR6784690", "SRX3744228", "SRS3000696", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 3 hpf whole embryo injected with TUT47MO Exp. ID: rs2", "GSM3024082", null, "tissue:Zebrafish whole embryo|hpf translation blocking  TUT7 translation blocking|strain:AB", "Zebrafish 3 hpf whole embryo injected with TUT47MO Exp. ID: rs2", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking  TUT7 translation blocking|strain:AB", "GSM3024082", "GSM3024082: Zebrafish 3 hpf whole embryo injected with TUT47MO Exp. ID: rs2; Danio rerio; RNA Seq", "GSM3024082", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs2-TUT47MO-3hpf_R1.fastq.gz rs2-TUT47MO-3hpf_R2.fastq.gz", "fastq fastq", 5793171744.0, 38112972.0, "GSM3024082 r1", "0:76 1:76", "A:1406452628;C:1469719832;G:1468022600;T:1447279036;N:1697648", 76, 76, null, null, 1406452628, 1469719832, 1468022600, 1447279036, 1697648, "SRX3744228", "SRS3000696", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95626, 0.95636, 0.07094, 0.0679, 0.76098, 0.76219, 0.59322, 0.59334, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47619, "SRR6784689", "SRX3744227", "SRS3000695", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 5 hpf whole embryo injected with ConMO Exp. ID: rs2", "GSM3024081", null, "tissue:Zebrafish whole embryo|hpf", "Zebrafish 5 hpf whole embryo injected with ConMO Exp. ID: rs2", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf", "GSM3024081", "GSM3024081: Zebrafish 5 hpf whole embryo injected with ConMO Exp. ID: rs2; Danio rerio; RNA Seq", "GSM3024081", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs2-ConMO-5hpf_R1.fastq.gz rs2-ConMO-5hpf_R2.fastq.gz", "fastq fastq", 6789240664.0, 44666057.0, "GSM3024081 r1", "0:76 1:76", "A:1692447747;C:1683205250;G:1674097638;T:1737501588;N:1988441", 76, 76, null, null, 1692447747, 1683205250, 1674097638, 1737501588, 1988441, "SRX3744227", "SRS3000695", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.93365, 0.93288, 0.18031, 0.17541, 0.75601, 0.75801, 0.51533, 0.59789, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47620, "SRR6784688", "SRX3744226", "SRS3000694", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 3 hpf whole embryo injected with ConMO Exp. ID: rs2", "GSM3024080", null, "tissue:Zebrafish whole embryo|hpf", "Zebrafish 3 hpf whole embryo injected with ConMO Exp. ID: rs2", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf", "GSM3024080", "GSM3024080: Zebrafish 3 hpf whole embryo injected with ConMO Exp. ID: rs2; Danio rerio; RNA Seq", "GSM3024080", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024080", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs2-ConMO-3hpf_R1.fastq.gz rs2-ConMO-3hpf_R2.fastq.gz", "fastq fastq", 7456939576.0, 49058813.0, "GSM3024080 r1", "0:76 1:76", "A:1813253495;C:1892010922;G:1885775058;T:1863713907;N:2186194", 76, 76, null, null, 1813253495, 1892010922, 1885775058, 1863713907, 2186194, "SRX3744226", "SRS3000694", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.94906, 0.95288, 0.06949, 0.06558, 0.75749, 0.75893, 0.57185, 0.59121, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47622, "SRR6784686", "SRX3744224", "SRS3000698", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 3 hpf whole embryo injected with TUT47MO Exp. ID: rs1b", "GSM3024078", null, "tissue:Zebrafish whole embryo|hpf translation blocking  TUT7 translation blocking|strain:AB", "Zebrafish 3 hpf whole embryo injected with TUT47MO Exp. ID: rs1b", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking  TUT7 translation blocking|strain:AB", "GSM3024078", "GSM3024078: Zebrafish 3 hpf whole embryo injected with TUT47MO Exp. ID: rs1b; Danio rerio; RNA Seq", "GSM3024078", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024078", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1b-TUT47MO-3hpf_R1.fastq.gz rs1b-TUT47MO-3hpf_R2.fastq.gz", "fastq fastq", 3512955750.0, 23419705.0, "GSM3024078 r1", "0:75 1:75", "A:904272993;C:846189136;G:845724027;T:914848835;N:1920759", 75, 75, null, null, 904272993, 846189136, 845724027, 914848835, 1920759, "SRX3744224", "SRS3000698", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.94996, 0.95308, 0.06884, 0.06709, 0.74546, 0.74856, 0.49941, 0.49729, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47624, "SRR6784684", "SRX3744222", "SRS3000691", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 3 hpf whole embryo injected with ConMO Exp. ID: rs1b", "GSM3024076", null, "tissue:Zebrafish whole embryo|hpf", "Zebrafish 3 hpf whole embryo injected with ConMO Exp. ID: rs1b", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf", "GSM3024076", "GSM3024076: Zebrafish 3 hpf whole embryo injected with ConMO Exp. ID: rs1b; Danio rerio; RNA Seq", "GSM3024076", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024076", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1b-ConMO-3hpf_R1.fastq.gz rs1b-ConMO-3hpf_R2.fastq.gz", "fastq fastq", 3588228600.0, 23921524.0, "GSM3024076 r1", "0:75 1:75", "A:927704680;C:861896753;G:859653360;T:937028832;N:1944975", 75, 75, null, null, 927704680, 861896753, 859653360, 937028832, 1944975, "SRX3744222", "SRS3000691", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.9482, 0.95265, 0.06761, 0.06634, 0.74673, 0.74949, 0.5033, 0.50552, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47626, "SRR6784682", "SRX3744220", "SRS3000689", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 4 hpf whole embryo injected with TUT47MO Exp. ID: rs1a", "GSM3024074", null, "tissue:Zebrafish whole embryo|hpf translation blocking  TUT7 translation blocking|strain:AB", "Zebrafish 4 hpf whole embryo injected with TUT47MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking  TUT7 translation blocking|strain:AB", "GSM3024074", "GSM3024074: Zebrafish 4 hpf whole embryo injected with TUT47MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024074", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024074", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT47MO-4hpf_R1.fastq.gz rs1a-TUT47MO-4hpf_R2.fastq.gz", "fastq fastq", 4012253850.0, 26748359.0, "GSM3024074 r1", "0:75 1:75", "A:1083176195;C:921754621;G:910925804;T:1094191077;N:2206153", 75, 75, null, null, 1083176195, 921754621, 910925804, 1094191077, 2206153, "SRX3744220", "SRS3000689", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95565, 0.96284, 0.08391, 0.08319, 0.75923, 0.76098, 0.72617, 0.72687, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47629, "SRR6784679", "SRX3744217", "SRS3000686", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 4 hpf whole embryo injected with TUT7MO Exp. ID: rs1a", "GSM3024071", null, "tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB", "Zebrafish 4 hpf whole embryo injected with TUT7MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking|strain:AB", "GSM3024071", "GSM3024071: Zebrafish 4 hpf whole embryo injected with TUT7MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024071", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT7MO-4hpf_R2.fastq.gz rs1a-TUT7MO-4hpf_R1.fastq.gz", "fastq fastq", 5768921100.0, 38459474.0, "GSM3024071 r1", "0:75 1:75", "A:1555172603;C:1327529056;G:1315409284;T:1567647314;N:3162843", 75, 75, null, null, 1555172603, 1327529056, 1315409284, 1567647314, 3162843, "SRX3744217", "SRS3000686", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95735, 0.96309, 0.08315, 0.08265, 0.76493, 0.76806, 0.72767, 0.73332, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47632, "SRR6784676", "SRX3744214", "SRS3000683", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 4 hpf whole embryo injected with TUT4MO Exp. ID: rs1a", "GSM3024068", null, "tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB", "Zebrafish 4 hpf whole embryo injected with TUT4MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking|strain:AB", "GSM3024068", "GSM3024068: Zebrafish 4 hpf whole embryo injected with TUT4MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024068", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024068", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT4MO-4hpf_R2.fastq.gz rs1a-TUT4MO-4hpf_R1.fastq.gz", "fastq fastq", 4215564300.0, 28103762.0, "GSM3024068 r1", "0:75 1:75", "A:1065121902;C:1041520955;G:1038600008;T:1068046442;N:2274993", 75, 75, null, null, 1065121902, 1041520955, 1038600008, 1068046442, 2274993, "SRX3744214", "SRS3000683", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.94653, 0.95013, 0.10969, 0.10755, 0.75469, 0.75777, 0.64019, 0.6461, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [47635, "SRR6784673", "SRX3744211", "SRS3000680", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 4 hpf whole embryo injected with ConMO Exp. ID: rs1a", "GSM3024065", null, "tissue:Zebrafish whole embryo|hpf", "Zebrafish 4 hpf whole embryo injected with ConMO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf", "GSM3024065", "GSM3024065: Zebrafish 4 hpf whole embryo injected with ConMO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024065", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-ConMO-4hpf_R2.fastq.gz rs1a-ConMO-4hpf_R1.fastq.gz", "fastq fastq", 3861279450.0, 25741863.0, "GSM3024065 r1", "0:75 1:75", "A:973485072;C:956743877;G:950463164;T:978475358;N:2111979", 75, 75, null, null, 973485072, 956743877, 950463164, 978475358, 2111979, "SRX3744211", "SRS3000680", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.9482, 0.95259, 0.11181, 0.10881, 0.7555, 0.75763, 0.64284, 0.64083, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [53282, "SRR11869572", "SRX8419562", "SRS6731106", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa s 3", "GSM4577399", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "mondoa s 3", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts exon.txt  exonic counts for each indicated gene and  sample", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "GSM4577399", "GSM4577399: F mondoa s 3; Danio rerio; RNA Seq", "GSM4577399", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM4577399", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN25_S2.R1.fastq VRGN25_S2.R2.fastq", "fastq fastq", 7551918900.0, 75519189.0, "GSM4577399 r1", "0:50 1:50", "A:2066041718;C:1702385113;G:1686618839;T:2095697396;N:1175834", 50, 50, null, null, 2066041718, 1702385113, 1686618839, 2095697396, 1175834, "SRX8419562", "SRS6731106", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.8972, 0.89917, 0.27419, 0.27338, 0.74576, 0.75668, 0.50768, 0.5128, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2020-05-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53283, "SRR11869571", "SRX8419561", "SRS6731105", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa s 2", "GSM4577398", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "mondoa s 2", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts exon.txt  exonic counts for each indicated gene and  sample", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "GSM4577398", "GSM4577398: E mondoa s 2; Danio rerio; RNA Seq", "GSM4577398", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM4577398", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN24_S2.R1.fastq VRGN24_S2.R2.fastq", "fastq fastq", 7666458300.0, 76664583.0, "GSM4577398 r1", "0:50 1:50", "A:2108884078;C:1705527841;G:1677597808;T:2173267709;N:1180864", 50, 50, null, null, 2108884078, 1705527841, 1677597808, 2173267709, 1180864, "SRX8419561", "SRS6731105", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89319, 0.89501, 0.29973, 0.29906, 0.74931, 0.75724, 0.50887, 0.50894, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2020-05-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53284, "SRR11869570", "SRX8419560", "SRS6731104", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa s 1", "GSM4577397", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "mondoa s 1", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts exon.txt  exonic counts for each indicated gene and  sample", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "GSM4577397", "GSM4577397: D mondoa s 1; Danio rerio; RNA Seq", "GSM4577397", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM4577397", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN23_S2.R1.fastq VRGN23_S2.R2.fastq", "fastq fastq", 6872302500.0, 68723025.0, "GSM4577397 r1", "0:50 1:50", "A:1873323778;C:1557060731;G:1546029001;T:1894832528;N:1056462", 50, 50, null, null, 1873323778, 1557060731, 1546029001, 1894832528, 1056462, "SRX8419560", "SRS6731104", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89976, 0.90345, 0.27147, 0.27139, 0.74957, 0.76187, 0.50583, 0.51168, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2020-05-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53285, "SRR9822880", "SRX6579572", "SRS5145283", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "WT n 3", "GSM3968576", null, "source name:total RNA|tissue:embryo|genotype:wild type|phenotype:unaffected epib|Stage:5 hpf", "WT n 3", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts mutants.txt: Tab delimited text file contains raw counts.", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:wild type|phenotype:unaffected epib|Stage:5 hpf", "GSM3968576", "GSM3968576: WT 3; Danio rerio; RNA Seq", "GSM3968576", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM3968576", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN28_S2.R1.fastq.gz VRGN28_S2.R2.fastq.gz", "fastq fastq", 8867395800.0, 88673958.0, "GSM3968576 r1", "0:50 1:50", "A:2377675533;C:2037155907;G:2034235985;T:2416929022;N:1399353", 50, 50, null, null, 2377675533, 2037155907, 2034235985, 2416929022, 1399353, "SRX6579572", "SRS5145283", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89244, 0.89367, 0.25364, 0.25177, 0.74562, 0.75071, 0.48724, 0.49306, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2019-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53286, "SRR9822879", "SRX6579571", "SRS5145282", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "WT n 2", "GSM3968575", null, "source name:total RNA|tissue:embryo|genotype:wild type|phenotype:unaffected epib|Stage:5 hpf", "WT n 2", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts mutants.txt: Tab delimited text file contains raw counts.", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:wild type|phenotype:unaffected epib|Stage:5 hpf", "GSM3968575", "GSM3968575: WT 2; Danio rerio; RNA Seq", "GSM3968575", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM3968575", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN27_S2.R1.fastq.gz VRGN27_S2.R2.fastq.gz", "fastq fastq", 8463600400.0, 84636004.0, "GSM3968575 r1", "0:50 1:50", "A:2302466173;C:1909305079;G:1886583111;T:2363912593;N:1333444", 50, 50, null, null, 2302466173, 1909305079, 1886583111, 2363912593, 1333444, "SRX6579571", "SRS5145282", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.88572, 0.88835, 0.29743, 0.29437, 0.74919, 0.75672, 0.49434, 0.49314, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2019-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53287, "SRR9822878", "SRX6579570", "SRS5145281", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "WT n 1", "GSM3968574", null, "source name:total RNA|tissue:embryo|genotype:wild type|phenotype:unaffected epib|Stage:5 hpf", "WT n 1", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts mutants.txt: Tab delimited text file contains raw counts.", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:wild type|phenotype:unaffected epib|Stage:5 hpf", "GSM3968574", "GSM3968574: WT 1; Danio rerio; RNA Seq", "GSM3968574", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM3968574", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN26_S2.R1.fastq.gz VRGN26_S2.R2.fastq.gz", "fastq fastq", 7628784300.0, 76287843.0, "GSM3968574 r1", "0:50 1:50", "A:2078754408;C:1719651241;G:1693975000;T:2135219453;N:1184198", 50, 50, null, null, 2078754408, 1719651241, 1693975000, 2135219453, 1184198, "SRX6579570", "SRS5145281", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89762, 0.89981, 0.30018, 0.29512, 0.74059, 0.74846, 0.48922, 0.49838, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2019-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53288, "SRR9822877", "SRX6579569", "SRS5145280", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa n 3", "GSM3968573", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:unaffected epib|Stage:5 hpf", "mondoa n 3", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts mutants.txt: Tab delimited text file contains raw counts.", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:unaffected epib|Stage:5 hpf", "GSM3968573", "GSM3968573: mondoa 3; Danio rerio; RNA Seq", "GSM3968573", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM3968573", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN25_S2.R2.fastq.gz VRGN25_S2.R1.fastq.gz", "fastq fastq", 7551918900.0, 75519189.0, "GSM3968573 r1", "0:50 1:50", "A:2066041718;C:1702385113;G:1686618839;T:2095697396;N:1175834", 50, 50, null, null, 2066041718, 1702385113, 1686618839, 2095697396, 1175834, "SRX6579569", "SRS5145280", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89704, 0.89919, 0.27361, 0.27325, 0.74637, 0.75755, 0.50569, 0.5107, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2019-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53289, "SRR9822876", "SRX6579568", "SRS5145279", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa n 2", "GSM3968572", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:unaffected epib|Stage:5 hpf", "mondoa n 2", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts mutants.txt: Tab delimited text file contains raw counts.", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:unaffected epib|Stage:5 hpf", "GSM3968572", "GSM3968572: mondoa 2; Danio rerio; RNA Seq", "GSM3968572", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM3968572", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN24_S2.R1.fastq.gz VRGN24_S2.R2.fastq.gz", "fastq fastq", 7666458300.0, 76664583.0, "GSM3968572 r1", "0:50 1:50", "A:2108884078;C:1705527841;G:1677597808;T:2173267709;N:1180864", 50, 50, null, null, 2108884078, 1705527841, 1677597808, 2173267709, 1180864, "SRX6579568", "SRS5145279", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89316, 0.89507, 0.29969, 0.29911, 0.74947, 0.75741, 0.50817, 0.50943, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2019-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53290, "SRR9822875", "SRX6579567", "SRS5145278", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa n 1", "GSM3968571", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:unaffected epib|Stage:5 hpf", "mondoa n 1", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts mutants.txt: Tab delimited text file contains raw counts.", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:unaffected epib|Stage:5 hpf", "GSM3968571", "GSM3968571: mondoa 1; Danio rerio; RNA Seq", "GSM3968571", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM3968571", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN23_S2.R2.fastq.gz VRGN23_S2.R1.fastq.gz", "fastq fastq", 6872302500.0, 68723025.0, "GSM3968571 r1", "0:50 1:50", "A:1873323778;C:1557060731;G:1546029001;T:1894832528;N:1056462", 50, 50, null, null, 1873323778, 1557060731, 1546029001, 1894832528, 1056462, "SRX6579567", "SRS5145278", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89971, 0.90355, 0.27138, 0.27147, 0.7501, 0.76185, 0.50874, 0.51203, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2019-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56025, "SRR10836792", "SRX7508634", "SRS5949026", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Cyt", "GSM4252155", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "Dome Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "GSM4252155", "GSM4252155: Dome Cyt; Danio rerio; RNA Seq", "GSM4252155", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252155", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-C2_L001_R2_001.fastq.gz Dome-C2_L001_R1_001.fastq.gz", "fastq fastq", 1600183273.0, 10609142.0, "GSM4252155 r1", "0:75.47 1:75.36", "A:406319131;C:381620266;G:406104578;T:405721915;N:417383", 75, 75, null, null, 406319131, 381620266, 406104578, 405721915, 417383, "SRX7508634", "SRS5949026", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.88183, 0.88249, 0.10573, 0.10435, 0.75481, 0.76033, 0.65717, 0.6586, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56026, "SRR10836793", "SRX7508634", "SRS5949026", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Cyt", "GSM4252155", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "Dome Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "GSM4252155", "GSM4252155: Dome Cyt; Danio rerio; RNA Seq", "GSM4252155", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252155", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-C2_L002_R1_001.fastq.gz Dome-C2_L002_R2_001.fastq.gz", "fastq fastq", 1566311827.0, 10384368.0, "GSM4252155 r2", "0:75.48 1:75.36", "A:398043893;C:372803129;G:397876607;T:397120910;N:467288", 75, 75, null, null, 398043893, 372803129, 397876607, 397120910, 467288, "SRX7508634", "SRS5949026", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.8823, 0.88437, 0.10602, 0.10527, 0.75564, 0.76118, 0.65836, 0.66025, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56027, "SRR10836794", "SRX7508634", "SRS5949026", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Cyt", "GSM4252155", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "Dome Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "GSM4252155", "GSM4252155: Dome Cyt; Danio rerio; RNA Seq", "GSM4252155", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252155", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-C2_L003_R1_001.fastq.gz Dome-C2_L003_R2_001.fastq.gz", "fastq fastq", 1594543994.0, 10571557.0, "GSM4252155 r3", "0:75.47 1:75.36", "A:405942855;C:382158076;G:399619556;T:406535479;N:288028", 75, 75, null, null, 405942855, 382158076, 399619556, 406535479, 288028, "SRX7508634", "SRS5949026", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.88258, 0.88139, 0.10614, 0.10462, 0.754, 0.75919, 0.3912, 0.65984, 73, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56028, "SRR10836795", "SRX7508634", "SRS5949026", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Cyt", "GSM4252155", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "Dome Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Cytosolic", "GSM4252155", "GSM4252155: Dome Cyt; Danio rerio; RNA Seq", "GSM4252155", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252155", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-C2_L004_R2_001.fastq.gz Dome-C2_L004_R1_001.fastq.gz", "fastq fastq", 1561211427.0, 10350323.0, "GSM4252155 r4", "0:75.48 1:75.36", "A:397911507;C:374246496;G:390504606;T:398280725;N:268093", 75, 75, null, null, 397911507, 374246496, 390504606, 398280725, 268093, "SRX7508634", "SRS5949026", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.88303, 0.88191, 0.1066, 0.10452, 0.75592, 0.76, 0.65797, 0.65812, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56029, "SRR10836788", "SRX7508633", "SRS5949025", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Nuc", "GSM4252154", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "Dome Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "GSM4252154", "GSM4252154: Dome Nuc; Danio rerio; RNA Seq", "GSM4252154", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252154", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-N2_L001_R1_001.fastq.gz Dome-N2_L001_R2_001.fastq.gz", "fastq fastq", 2074718856.0, 13753362.0, "GSM4252154 r1", "0:75.47 1:75.38", "A:548207869;C:474119517;G:498330967;T:553614124;N:446379", 75, 75, null, null, 548207869, 474119517, 498330967, 553614124, 446379, "SRX7508633", "SRS5949025", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.92904, 0.93027, 0.25794, 0.25635, 0.73314, 0.73543, 0.63799, 0.63772, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56030, "SRR10836789", "SRX7508633", "SRS5949025", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Nuc", "GSM4252154", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "Dome Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "GSM4252154", "GSM4252154: Dome Nuc; Danio rerio; RNA Seq", "GSM4252154", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252154", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-N2_L002_R1_001.fastq.gz Dome-N2_L002_R2_001.fastq.gz", "fastq fastq", 2029358370.0, 13452695.0, "GSM4252154 r2", "0:75.47 1:75.38", "A:536416032;C:463133536;G:487927693;T:541364778;N:516331", 75, 75, null, null, 536416032, 463133536, 487927693, 541364778, 516331, "SRX7508633", "SRS5949025", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.92826, 0.93051, 0.25765, 0.25606, 0.73294, 0.73537, 0.63631, 0.63767, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56031, "SRR10836790", "SRX7508633", "SRS5949025", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Nuc", "GSM4252154", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "Dome Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "GSM4252154", "GSM4252154: Dome Nuc; Danio rerio; RNA Seq", "GSM4252154", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252154", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-N2_L003_R1_001.fastq.gz Dome-N2_L003_R2_001.fastq.gz", "fastq fastq", 2071038727.0, 13728438.0, "GSM4252154 r3", "0:75.47 1:75.38", "A:549024994;C:475436351;G:490887464;T:555409952;N:279966", 75, 75, null, null, 549024994, 475436351, 490887464, 555409952, 279966, "SRX7508633", "SRS5949025", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.92832, 0.92953, 0.25562, 0.25507, 0.73253, 0.73523, 0.64216, 0.64054, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56032, "SRR10836791", "SRX7508633", "SRS5949025", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "Dome Nuc", "GSM4252154", null, "source name:Dome stage embryo|tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "Dome Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "Dome stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:Dome|fraction:Nuclear", "GSM4252154", "GSM4252154: Dome Nuc; Danio rerio; RNA Seq", "GSM4252154", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252154", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "Dome-N2_L004_R1_001.fastq.gz Dome-N2_L004_R2_001.fastq.gz", "fastq fastq", 2029324602.0, 13451857.0, "GSM4252154 r4", "0:75.47 1:75.38", "A:538432870;C:466166947;G:479781700;T:544692254;N:250831", 75, 75, null, null, 538432870, 466166947, 479781700, 544692254, 250831, "SRX7508633", "SRS5949025", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.92876, 0.93022, 0.25694, 0.25536, 0.73186, 0.73501, 0.64101, 0.64, 74, 73, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56033, "SRR10836784", "SRX7508632", "SRS5949024", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Cyt", "GSM4252153", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "1000 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "GSM4252153", "GSM4252153: 1000 cell Cyt; Danio rerio; RNA Seq", "GSM4252153", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252153", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-C2_L001_R1_001.fastq.gz 1000-Cell-C2_L001_R2_001.fastq.gz", "fastq fastq", 1502587165.0, 9955261.0, "GSM4252153 r1", "0:75.54 1:75.39", "A:375894288;C:354892799;G:392076871;T:379250340;N:472867", 75, 75, null, null, 375894288, 354892799, 392076871, 379250340, 472867, "SRX7508632", "SRS5949024", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95863, 0.95851, 0.05633, 0.05543, 0.76171, 0.76495, 0.61191, 0.62248, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56034, "SRR10836785", "SRX7508632", "SRS5949024", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Cyt", "GSM4252153", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "1000 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "GSM4252153", "GSM4252153: 1000 cell Cyt; Danio rerio; RNA Seq", "GSM4252153", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252153", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-C2_L002_R1_001.fastq.gz 1000-Cell-C2_L002_R2_001.fastq.gz", "fastq fastq", 1457310394.0, 9656279.0, "GSM4252153 r2", "0:75.53 1:75.38", "A:368230607;C:346079382;G:372752678;T:369738027;N:509700", 75, 75, null, null, 368230607, 346079382, 372752678, 369738027, 509700, "SRX7508632", "SRS5949024", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.96005, 0.95978, 0.05635, 0.05584, 0.76181, 0.76449, 0.61792, 0.61931, 71, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56035, "SRR10836786", "SRX7508632", "SRS5949024", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Cyt", "GSM4252153", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "1000 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "GSM4252153", "GSM4252153: 1000 cell Cyt; Danio rerio; RNA Seq", "GSM4252153", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252153", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-C2_L003_R1_001.fastq.gz 1000-Cell-C2_L003_R2_001.fastq.gz", "fastq fastq", 1483084690.0, 9826007.0, "GSM4252153 r3", "0:75.54 1:75.40", "A:373953592;C:352136477;G:380681829;T:376135696;N:177096", 75, 75, null, null, 373953592, 352136477, 380681829, 376135696, 177096, "SRX7508632", "SRS5949024", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95919, 0.95984, 0.05678, 0.05526, 0.7611, 0.76366, 0.62126, 0.62066, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56036, "SRR10836787", "SRX7508632", "SRS5949024", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Cyt", "GSM4252153", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "1000 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Cytosolic", "GSM4252153", "GSM4252153: 1000 cell Cyt; Danio rerio; RNA Seq", "GSM4252153", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252153", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-C2_L004_R1_001.fastq.gz 1000-Cell-C2_L004_R2_001.fastq.gz", "fastq fastq", 1429141217.0, 9469098.0, "GSM4252153 r4", "0:75.53 1:75.40", "A:363231227;C:342106867;G:358226946;T:365368980;N:207197", 75, 75, null, null, 363231227, 342106867, 358226946, 365368980, 207197, "SRX7508632", "SRS5949024", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95926, 0.95888, 0.05715, 0.05517, 0.76096, 0.76469, 0.62196, 0.39902, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56037, "SRR10836780", "SRX7508631", "SRS5949023", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Nuc", "GSM4252152", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "1000 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "GSM4252152", "GSM4252152: 1000 cell Nuc; Danio rerio; RNA Seq", "GSM4252152", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252152", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-N2_L001_R2_001.fastq.gz 1000-Cell-N2_L001_R1_001.fastq.gz", "fastq fastq", 1595563955.0, 10573494.0, "GSM4252152 r1", "0:75.54 1:75.36", "A:421378481;C:358086779;G:389857864;T:425749482;N:491349", 75, 75, null, null, 421378481, 358086779, 389857864, 425749482, 491349, "SRX7508631", "SRS5949023", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95517, 0.95344, 0.06181, 0.06032, 0.77646, 0.7807, 0.76076, 0.75765, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56038, "SRR10836781", "SRX7508631", "SRS5949023", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Nuc", "GSM4252152", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "1000 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "GSM4252152", "GSM4252152: 1000 cell Nuc; Danio rerio; RNA Seq", "GSM4252152", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252152", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-N2_L002_R1_001.fastq.gz 1000-Cell-N2_L002_R2_001.fastq.gz", "fastq fastq", 1548947081.0, 10265666.0, "GSM4252152 r2", "0:75.54 1:75.35", "A:412283151;C:349200776;G:371851315;T:415086710;N:525129", 75, 75, null, null, 412283151, 349200776, 371851315, 415086710, 525129, "SRX7508631", "SRS5949023", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95432, 0.9535, 0.06288, 0.06218, 0.77617, 0.78027, 0.75937, 0.75829, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56039, "SRR10836782", "SRX7508631", "SRS5949023", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Nuc", "GSM4252152", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "1000 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "GSM4252152", "GSM4252152: 1000 cell Nuc; Danio rerio; RNA Seq", "GSM4252152", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252152", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-N2_L003_R1_001.fastq.gz 1000-Cell-N2_L003_R2_001.fastq.gz", "fastq fastq", 1577107128.0, 10451104.0, "GSM4252152 r3", "0:75.54 1:75.36", "A:419102048;C:355504687;G:379988890;T:422345890;N:165613", 75, 75, null, null, 419102048, 355504687, 379988890, 422345890, 165613, "SRX7508631", "SRS5949023", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95405, 0.95325, 0.06249, 0.06213, 0.7766, 0.78027, 0.76255, 0.76017, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56040, "SRR10836783", "SRX7508631", "SRS5949023", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "1000 cell Nuc", "GSM4252152", null, "source name:1000Cell stage embryo|tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "1000 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "1000Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:1000 cell|fraction:Nuclear", "GSM4252152", "GSM4252152: 1000 cell Nuc; Danio rerio; RNA Seq", "GSM4252152", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252152", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "1000-Cell-N2_L004_R1_001.fastq.gz 1000-Cell-N2_L004_R2_001.fastq.gz", "fastq fastq", 1529237226.0, 10134567.0, "GSM4252152 r4", "0:75.53 1:75.36", "A:409232864;C:346856483;G:360903103;T:412045187;N:199589", 75, 75, null, null, 409232864, 346856483, 360903103, 412045187, 199589, "SRX7508631", "SRS5949023", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.95294, 0.95308, 0.06214, 0.06138, 0.77518, 0.77883, 0.76284, 0.76063, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56041, "SRR10836776", "SRX7508630", "SRS5949022", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Cyt", "GSM4252151", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "256 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "GSM4252151", "GSM4252151: 256 cell Cyt; Danio rerio; RNA Seq", "GSM4252151", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252151", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-C2_L001_R1_001.fastq.gz 256-Cell-C2_L001_R2_001.fastq.gz", "fastq fastq", 1366272364.0, 9052072.0, "GSM4252151 r1", "0:75.51 1:75.42", "A:323814430;C:338855107;G:375548122;T:327579283;N:475422", 75, 75, null, null, 323814430, 338855107, 375548122, 327579283, 475422, "SRX7508630", "SRS5949022", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.83802, 0.8313, 0.07237, 0.06855, 0.77352, 0.77611, 0.60128, 0.59485, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56042, "SRR10836777", "SRX7508630", "SRS5949022", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Cyt", "GSM4252151", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "256 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "GSM4252151", "GSM4252151: 256 cell Cyt; Danio rerio; RNA Seq", "GSM4252151", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252151", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-C2_L002_R1_001.fastq.gz 256-Cell-C2_L002_R2_001.fastq.gz", "fastq fastq", 1327435639.0, 8795964.0, "GSM4252151 r2", "0:75.50 1:75.41", "A:318150528;C:331260745;G:357195153;T:320310778;N:518435", 75, 75, null, null, 318150528, 331260745, 357195153, 320310778, 518435, "SRX7508630", "SRS5949022", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.83323, 0.82627, 0.07204, 0.06736, 0.77169, 0.77437, 0.60689, 0.5972, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56043, "SRR10836778", "SRX7508630", "SRS5949022", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Cyt", "GSM4252151", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "256 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "GSM4252151", "GSM4252151: 256 cell Cyt; Danio rerio; RNA Seq", "GSM4252151", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252151", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-C2_L003_R1_001.fastq.gz 256-Cell-C2_L003_R2_001.fastq.gz", "fastq fastq", 1349181703.0, 8939006.0, "GSM4252151 r3", "0:75.51 1:75.43", "A:322588049;C:336503258;G:364782594;T:325107660;N:200142", 75, 75, null, null, 322588049, 336503258, 364782594, 325107660, 200142, "SRX7508630", "SRS5949022", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.83327, 0.82509, 0.07273, 0.06804, 0.7736, 0.77597, 0.61092, 0.59732, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56044, "SRR10836779", "SRX7508630", "SRS5949022", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Cyt", "GSM4252151", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "256 cell Cyt", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Cytosolic", "GSM4252151", "GSM4252151: 256 cell Cyt; Danio rerio; RNA Seq", "GSM4252151", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252151", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-C2_L004_R1_001.fastq.gz 256-Cell-C2_L004_R2_001.fastq.gz", "fastq fastq", 1303623813.0, 8637679.0, "GSM4252151 r4", "0:75.50 1:75.42", "A:314181485;C:328280077;G:344028018;T:316907421;N:226812", 75, 75, null, null, 314181485, 328280077, 344028018, 316907421, 226812, "SRX7508630", "SRS5949022", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.82898, 0.82179, 0.07137, 0.06711, 0.77177, 0.775, 0.60119, 0.59652, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56045, "SRR10836772", "SRX7508629", "SRS5949021", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Nuc", "GSM4252150", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "256 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "GSM4252150", "GSM4252150: 256 cell Nuc; Danio rerio; RNA Seq", "GSM4252150", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252150", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-N2_L001_R2_001.fastq.gz 256-Cell-N2_L001_R1_001.fastq.gz", "fastq fastq", 1628475646.0, 10788030.0, "GSM4252150 r1", "0:75.57 1:75.38", "A:425213330;C:378434245;G:395256706;T:429054367;N:516998", 75, 75, null, null, 425213330, 378434245, 395256706, 429054367, 516998, "SRX7508629", "SRS5949021", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.91766, 0.91401, 0.04416, 0.04189, 0.79849, 0.79961, 0.80261, 0.79877, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56046, "SRR10836773", "SRX7508629", "SRS5949021", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Nuc", "GSM4252150", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "256 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "GSM4252150", "GSM4252150: 256 cell Nuc; Danio rerio; RNA Seq", "GSM4252150", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252150", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-N2_L002_R1_001.fastq.gz 256-Cell-N2_L002_R2_001.fastq.gz", "fastq fastq", 1582693274.0, 10485714.0, "GSM4252150 r2", "0:75.56 1:75.38", "A:415594410;C:368965826;G:379347535;T:418234862;N:550641", 75, 75, null, null, 415594410, 368965826, 379347535, 418234862, 550641, "SRX7508629", "SRS5949021", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.91631, 0.91267, 0.04442, 0.04195, 0.79638, 0.79853, 0.8003, 0.79303, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56047, "SRR10836774", "SRX7508629", "SRS5949021", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Nuc", "GSM4252150", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "256 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "GSM4252150", "GSM4252150: 256 cell Nuc; Danio rerio; RNA Seq", "GSM4252150", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252150", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-N2_L003_R1_001.fastq.gz 256-Cell-N2_L003_R2_001.fastq.gz", "fastq fastq", 1606644595.0, 10643266.0, "GSM4252150 r3", "0:75.57 1:75.39", "A:421472450;C:374504298;G:386000123;T:424481255;N:186469", 75, 75, null, null, 421472450, 374504298, 386000123, 424481255, 186469, "SRX7508629", "SRS5949021", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.9166, 0.91216, 0.04398, 0.04143, 0.79817, 0.79969, 0.8036, 0.25479, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56048, "SRR10836775", "SRX7508629", "SRS5949021", "SRP239626", "PRJNA599208", "Genome wide localization of RNAs during early zebrafish development", "GSE143208", "Transcriptome Analysis", "We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.", null, "pubmed:33795334", null, "256 cell Nuc", "GSM4252150", null, "source name:256Cell stage embryo|tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "256 cell Nuc", "RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages", "256Cell stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|developmental stage:256 cell|fraction:Nuclear", "GSM4252150", "GSM4252150: 256 cell Nuc; Danio rerio; RNA Seq", "GSM4252150", null, "1", "RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.", "GEO Accession:GSM4252150", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP239626", null, null, "256-Cell-N2_L004_R1_001.fastq.gz 256-Cell-N2_L004_R2_001.fastq.gz", "fastq fastq", 1556236261.0, 10309792.0, "GSM4252150 r4", "0:75.56 1:75.39", "A:410297368;C:364669857;G:367737181;T:413315089;N:216766", 75, 75, null, null, 410297368, 364669857, 367737181, 413315089, 216766, "SRX7508629", "SRS5949021", "SRA1020776", "GEO", "School of Biosciences, University of Birmingham", 2, 0.91475, 0.91068, 0.04464, 0.04249, 0.7974, 0.79878, 0.80334, 0.7997, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-01-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [57241, "SRR11293510", "SRX7899072", "SRS6307327", "SRP252498", "PRJNA612134", "Targeted RNA Knockdown by a Type III CRISPR Cas Complex in Zebrafish", "GSE146852", "Transcriptome Analysis", "RNA interference RNAi is a powerful experimental tool for RNA knockdown  but not all organisms are amenable. Here  we provide a \u201cproof of principle\u201d demonstration that CRISPR endoribonuclease can be used for programmable mRNA transcript degradation in eukaryotes. Using zebrafish as the animal model and Csm complex as the CRISPR endoribonuclease  we targeted EGFP transcript expressed from a variety of promoters. A drastic decrease of fluorescence was achieved in germ cells of the vasa:EGFP line. Weaker effects were also seen in fish lines that express EGFP zygotically. Knockdown was statistically significant in cmcl2:EGFP and fli1:EGFP zebrafish lines at 1 dpf dpf  but reduced to background levels at 2 dpf. The nkx2.5:EGFP fish line was least susceptible to Csm mediated EGFP knockdown. We also tested Csm mediated knockdown on the endogenous tdgf1 oep transcript. At optimal Csm dose  we observed a penetrance of the characteristic one eyed phenotype at greater than 50% penetrance  and hence with similar efficiency to morpholino mediated knockdown. We conclude that Csm mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts  in some cases reaching comparable efficiency to morpholino based knockdown with no significant off target effects in our model. Overall design: Zebrafish embryos from the transgenic line Tgddx4:ddx4 EGFP on the background of ABTL were injected with the Csm complex targeted against the EGFP transcript or mock solution StCsm buffer without xxx proteins. The RNA was isolated from the pooled embryos at three time points: 128 cell stage  5 hpf and 24 hpf. Three replicates were obtained from each experimental condition and time point. Pair end sequencing was performed on the Illumina NextSeq platform.", null, "pubmed:32833532", null, "Mock 5hpf Rep 3", "GSM4407869", null, "source name:whole zebrafish embryo|strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:5 hpf", "Mock 5hpf Rep 3", "Base calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. The first 12 nucleotides of read 1  containing the UMI sequence  were extracted and added to the sequence identifier using UMI tools v. 1.0.0. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters:   outFilterType BySJout   outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1   outFilterMismatchNmax 999   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   outFilterMismatchNoverLmax 0.6. Alignments were de duplicated based on their Unique Molecular Identifier sequence using UMI tools v. 1.0.0. De duplicated alignments were counted per exon on the gene level with the htseq count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation. Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package. Genome build: GRCz11 Supplementary files format and content: HTSeq counts.tsv files were generated with htseq count script  they contain counts for each gene for each sample in tab delimited format; normalized counts files were generated with DESeq2  they contain library size normalized read counts for each gene for every sample from each time point in tab delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.", "whole zebrafish embryo", "Zebrafish embryos from three different mating pairs of Tgddx4:ddx4 EGFP females with casper males were pooled during collection. D16A StCsmEGFP was diluted with water for injection 1:1 v/v up to a concentration of 0.7mg/ml. For mock injection  Tris storage buffer 10mM Tris HCl pH8.5  300mM Nacl  1mM DTT  0.1mM EDTA  50% glycerol was also diluted in the similar manner. 1nl of either StCsm EGFP solution 0.7ng or buffer alone were injected into the yolk of embryos at the 1 cell stage. In total  three independent injections were performed. 25 embryos for both StCsm and mock injected per replica set per time point were frozen in liquid nitrogen  stored at xxx\u2103  and processed together.", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer\u2019s protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer\u2019s protocol.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.", "strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:5 hpf", "GSM4407869", "GSM4407869: Mock 5hpf Rep 3; Danio rerio; RNA Seq", "GSM4407869", null, "1", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer's protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer's protocol.", "GEO Accession:GSM4407869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP252498", null, null, "Mock-5hpf-Rep-3_R1.fastq.gz Mock-5hpf-Rep-3_R2.fastq.gz", "fastq fastq", 2842544510.0, 21865727.0, "GSM4407869 r1", "0:71 1:59", "A:799747787;C:578455085;G:650943235;T:809456844;N:3941559", 71, 59, null, null, 799747787, 578455085, 650943235, 809456844, 3941559, "SRX7899072", "SRS6307327", "SRA1054182", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.60476, 0.47987, 0.07746, 0.06523, 0.76978, 0.79064, 0.53156, 0.5417, 71, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Poland", "2020-03-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [57242, "SRR11293509", "SRX7899071", "SRS6307331", "SRP252498", "PRJNA612134", "Targeted RNA Knockdown by a Type III CRISPR Cas Complex in Zebrafish", "GSE146852", "Transcriptome Analysis", "RNA interference RNAi is a powerful experimental tool for RNA knockdown  but not all organisms are amenable. Here  we provide a \u201cproof of principle\u201d demonstration that CRISPR endoribonuclease can be used for programmable mRNA transcript degradation in eukaryotes. Using zebrafish as the animal model and Csm complex as the CRISPR endoribonuclease  we targeted EGFP transcript expressed from a variety of promoters. A drastic decrease of fluorescence was achieved in germ cells of the vasa:EGFP line. Weaker effects were also seen in fish lines that express EGFP zygotically. Knockdown was statistically significant in cmcl2:EGFP and fli1:EGFP zebrafish lines at 1 dpf dpf  but reduced to background levels at 2 dpf. The nkx2.5:EGFP fish line was least susceptible to Csm mediated EGFP knockdown. We also tested Csm mediated knockdown on the endogenous tdgf1 oep transcript. At optimal Csm dose  we observed a penetrance of the characteristic one eyed phenotype at greater than 50% penetrance  and hence with similar efficiency to morpholino mediated knockdown. We conclude that Csm mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts  in some cases reaching comparable efficiency to morpholino based knockdown with no significant off target effects in our model. Overall design: Zebrafish embryos from the transgenic line Tgddx4:ddx4 EGFP on the background of ABTL were injected with the Csm complex targeted against the EGFP transcript or mock solution StCsm buffer without xxx proteins. The RNA was isolated from the pooled embryos at three time points: 128 cell stage  5 hpf and 24 hpf. Three replicates were obtained from each experimental condition and time point. Pair end sequencing was performed on the Illumina NextSeq platform.", null, "pubmed:32833532", null, "Mock 5hpf Rep 2", "GSM4407868", null, "source name:whole zebrafish embryo|strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:5 hpf", "Mock 5hpf Rep 2", "Base calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. The first 12 nucleotides of read 1  containing the UMI sequence  were extracted and added to the sequence identifier using UMI tools v. 1.0.0. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters:   outFilterType BySJout   outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1   outFilterMismatchNmax 999   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   outFilterMismatchNoverLmax 0.6. Alignments were de duplicated based on their Unique Molecular Identifier sequence using UMI tools v. 1.0.0. De duplicated alignments were counted per exon on the gene level with the htseq count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation. Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package. Genome build: GRCz11 Supplementary files format and content: HTSeq counts.tsv files were generated with htseq count script  they contain counts for each gene for each sample in tab delimited format; normalized counts files were generated with DESeq2  they contain library size normalized read counts for each gene for every sample from each time point in tab delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.", "whole zebrafish embryo", "Zebrafish embryos from three different mating pairs of Tgddx4:ddx4 EGFP females with casper males were pooled during collection. D16A StCsmEGFP was diluted with water for injection 1:1 v/v up to a concentration of 0.7mg/ml. For mock injection  Tris storage buffer 10mM Tris HCl pH8.5  300mM Nacl  1mM DTT  0.1mM EDTA  50% glycerol was also diluted in the similar manner. 1nl of either StCsm EGFP solution 0.7ng or buffer alone were injected into the yolk of embryos at the 1 cell stage. In total  three independent injections were performed. 25 embryos for both StCsm and mock injected per replica set per time point were frozen in liquid nitrogen  stored at xxx\u2103  and processed together.", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer\u2019s protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer\u2019s protocol.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.", "strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:5 hpf", "GSM4407868", "GSM4407868: Mock 5hpf Rep 2; Danio rerio; RNA Seq", "GSM4407868", null, "1", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer's protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer's protocol.", "GEO Accession:GSM4407868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP252498", null, null, "Mock-5hpf-Rep-2_R2.fastq.gz Mock-5hpf-Rep-2_R1.fastq.gz", "fastq fastq", 2568887880.0, 19760676.0, "GSM4407868 r1", "0:71 1:59", "A:734167827;C:503406924;G:571409098;T:756330561;N:3573470", 71, 59, null, null, 734167827, 503406924, 571409098, 756330561, 3573470, "SRX7899071", "SRS6307331", "SRA1054182", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.65779, 0.50537, 0.10242, 0.08466, 0.76759, 0.79492, 0.50601, 0.52295, 71, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Poland", "2020-03-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [57243, "SRR11293508", "SRX7899070", "SRS6307326", "SRP252498", "PRJNA612134", "Targeted RNA Knockdown by a Type III CRISPR Cas Complex in Zebrafish", "GSE146852", "Transcriptome Analysis", "RNA interference RNAi is a powerful experimental tool for RNA knockdown  but not all organisms are amenable. Here  we provide a \u201cproof of principle\u201d demonstration that CRISPR endoribonuclease can be used for programmable mRNA transcript degradation in eukaryotes. Using zebrafish as the animal model and Csm complex as the CRISPR endoribonuclease  we targeted EGFP transcript expressed from a variety of promoters. A drastic decrease of fluorescence was achieved in germ cells of the vasa:EGFP line. Weaker effects were also seen in fish lines that express EGFP zygotically. Knockdown was statistically significant in cmcl2:EGFP and fli1:EGFP zebrafish lines at 1 dpf dpf  but reduced to background levels at 2 dpf. The nkx2.5:EGFP fish line was least susceptible to Csm mediated EGFP knockdown. We also tested Csm mediated knockdown on the endogenous tdgf1 oep transcript. At optimal Csm dose  we observed a penetrance of the characteristic one eyed phenotype at greater than 50% penetrance  and hence with similar efficiency to morpholino mediated knockdown. We conclude that Csm mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts  in some cases reaching comparable efficiency to morpholino based knockdown with no significant off target effects in our model. Overall design: Zebrafish embryos from the transgenic line Tgddx4:ddx4 EGFP on the background of ABTL were injected with the Csm complex targeted against the EGFP transcript or mock solution StCsm buffer without xxx proteins. The RNA was isolated from the pooled embryos at three time points: 128 cell stage  5 hpf and 24 hpf. Three replicates were obtained from each experimental condition and time point. Pair end sequencing was performed on the Illumina NextSeq platform.", null, "pubmed:32833532", null, "Mock 5hpf Rep 1", "GSM4407867", null, "source name:whole zebrafish embryo|strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:5 hpf", "Mock 5hpf Rep 1", "Base calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. The first 12 nucleotides of read 1  containing the UMI sequence  were extracted and added to the sequence identifier using UMI tools v. 1.0.0. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters:   outFilterType BySJout   outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1   outFilterMismatchNmax 999   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   outFilterMismatchNoverLmax 0.6. Alignments were de duplicated based on their Unique Molecular Identifier sequence using UMI tools v. 1.0.0. De duplicated alignments were counted per exon on the gene level with the htseq count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation. Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package. Genome build: GRCz11 Supplementary files format and content: HTSeq counts.tsv files were generated with htseq count script  they contain counts for each gene for each sample in tab delimited format; normalized counts files were generated with DESeq2  they contain library size normalized read counts for each gene for every sample from each time point in tab delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.", "whole zebrafish embryo", "Zebrafish embryos from three different mating pairs of Tgddx4:ddx4 EGFP females with casper males were pooled during collection. D16A StCsmEGFP was diluted with water for injection 1:1 v/v up to a concentration of 0.7mg/ml. For mock injection  Tris storage buffer 10mM Tris HCl pH8.5  300mM Nacl  1mM DTT  0.1mM EDTA  50% glycerol was also diluted in the similar manner. 1nl of either StCsm EGFP solution 0.7ng or buffer alone were injected into the yolk of embryos at the 1 cell stage. In total  three independent injections were performed. 25 embryos for both StCsm and mock injected per replica set per time point were frozen in liquid nitrogen  stored at xxx\u2103  and processed together.", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer\u2019s protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer\u2019s protocol.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.", "strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:5 hpf", "GSM4407867", "GSM4407867: Mock 5hpf Rep 1; Danio rerio; RNA Seq", "GSM4407867", null, "1", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer's protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer's protocol.", "GEO Accession:GSM4407867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP252498", null, null, "Mock-5hpf-Rep-1_R1.fastq.gz Mock-5hpf-Rep-1_R2.fastq.gz", "fastq fastq", 3252464540.0, 25018958.0, "GSM4407867 r1", "0:71 1:59", "A:898913139;C:680806953;G:759240096;T:908987584;N:4516768", 71, 59, null, null, 898913139, 680806953, 759240096, 908987584, 4516768, "SRX7899070", "SRS6307326", "SRA1054182", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.60017, 0.47729, 0.08055, 0.06599, 0.78995, 0.81126, 0.57855, 0.58317, 71, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Poland", "2020-03-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [57247, "SRR11293504", "SRX7899066", "SRS6307322", "SRP252498", "PRJNA612134", "Targeted RNA Knockdown by a Type III CRISPR Cas Complex in Zebrafish", "GSE146852", "Transcriptome Analysis", "RNA interference RNAi is a powerful experimental tool for RNA knockdown  but not all organisms are amenable. Here  we provide a \u201cproof of principle\u201d demonstration that CRISPR endoribonuclease can be used for programmable mRNA transcript degradation in eukaryotes. Using zebrafish as the animal model and Csm complex as the CRISPR endoribonuclease  we targeted EGFP transcript expressed from a variety of promoters. A drastic decrease of fluorescence was achieved in germ cells of the vasa:EGFP line. Weaker effects were also seen in fish lines that express EGFP zygotically. Knockdown was statistically significant in cmcl2:EGFP and fli1:EGFP zebrafish lines at 1 dpf dpf  but reduced to background levels at 2 dpf. The nkx2.5:EGFP fish line was least susceptible to Csm mediated EGFP knockdown. We also tested Csm mediated knockdown on the endogenous tdgf1 oep transcript. At optimal Csm dose  we observed a penetrance of the characteristic one eyed phenotype at greater than 50% penetrance  and hence with similar efficiency to morpholino mediated knockdown. We conclude that Csm mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts  in some cases reaching comparable efficiency to morpholino based knockdown with no significant off target effects in our model. Overall design: Zebrafish embryos from the transgenic line Tgddx4:ddx4 EGFP on the background of ABTL were injected with the Csm complex targeted against the EGFP transcript or mock solution StCsm buffer without xxx proteins. The RNA was isolated from the pooled embryos at three time points: 128 cell stage  5 hpf and 24 hpf. Three replicates were obtained from each experimental condition and time point. Pair end sequencing was performed on the Illumina NextSeq platform.", null, "pubmed:32833532", null, "Mock 128 Rep 3", "GSM4407863", null, "source name:whole zebrafish embryo|strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:128 cells", "Mock 128 Rep 3", "Base calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. The first 12 nucleotides of read 1  containing the UMI sequence  were extracted and added to the sequence identifier using UMI tools v. 1.0.0. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters:   outFilterType BySJout   outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1   outFilterMismatchNmax 999   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   outFilterMismatchNoverLmax 0.6. Alignments were de duplicated based on their Unique Molecular Identifier sequence using UMI tools v. 1.0.0. De duplicated alignments were counted per exon on the gene level with the htseq count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation. Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package. Genome build: GRCz11 Supplementary files format and content: HTSeq counts.tsv files were generated with htseq count script  they contain counts for each gene for each sample in tab delimited format; normalized counts files were generated with DESeq2  they contain library size normalized read counts for each gene for every sample from each time point in tab delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.", "whole zebrafish embryo", "Zebrafish embryos from three different mating pairs of Tgddx4:ddx4 EGFP females with casper males were pooled during collection. D16A StCsmEGFP was diluted with water for injection 1:1 v/v up to a concentration of 0.7mg/ml. For mock injection  Tris storage buffer 10mM Tris HCl pH8.5  300mM Nacl  1mM DTT  0.1mM EDTA  50% glycerol was also diluted in the similar manner. 1nl of either StCsm EGFP solution 0.7ng or buffer alone were injected into the yolk of embryos at the 1 cell stage. In total  three independent injections were performed. 25 embryos for both StCsm and mock injected per replica set per time point were frozen in liquid nitrogen  stored at xxx\u2103  and processed together.", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer\u2019s protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer\u2019s protocol.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.", "strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:128 cells", "GSM4407863", "GSM4407863: Mock 128 Rep 3; Danio rerio; RNA Seq", "GSM4407863", null, "1", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer's protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer's protocol.", "GEO Accession:GSM4407863", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP252498", null, null, "Mock-128-Rep-3_R2.fastq.gz Mock-128-Rep-3_R1.fastq.gz", "fastq fastq", 3261013600.0, 25084720.0, "GSM4407863 r1", "0:71 1:59", "A:900737410;C:688855174;G:770946078;T:895944416;N:4530522", 71, 59, null, null, 900737410, 688855174, 770946078, 895944416, 4530522, "SRX7899066", "SRS6307322", "SRA1054182", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.57905, 0.4659, 0.03571, 0.0302, 0.77536, 0.79022, 0.5161, 0.51323, 71, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Poland", "2020-03-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [57248, "SRR11293503", "SRX7899065", "SRS6307321", "SRP252498", "PRJNA612134", "Targeted RNA Knockdown by a Type III CRISPR Cas Complex in Zebrafish", "GSE146852", "Transcriptome Analysis", "RNA interference RNAi is a powerful experimental tool for RNA knockdown  but not all organisms are amenable. Here  we provide a \u201cproof of principle\u201d demonstration that CRISPR endoribonuclease can be used for programmable mRNA transcript degradation in eukaryotes. Using zebrafish as the animal model and Csm complex as the CRISPR endoribonuclease  we targeted EGFP transcript expressed from a variety of promoters. A drastic decrease of fluorescence was achieved in germ cells of the vasa:EGFP line. Weaker effects were also seen in fish lines that express EGFP zygotically. Knockdown was statistically significant in cmcl2:EGFP and fli1:EGFP zebrafish lines at 1 dpf dpf  but reduced to background levels at 2 dpf. The nkx2.5:EGFP fish line was least susceptible to Csm mediated EGFP knockdown. We also tested Csm mediated knockdown on the endogenous tdgf1 oep transcript. At optimal Csm dose  we observed a penetrance of the characteristic one eyed phenotype at greater than 50% penetrance  and hence with similar efficiency to morpholino mediated knockdown. We conclude that Csm mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts  in some cases reaching comparable efficiency to morpholino based knockdown with no significant off target effects in our model. Overall design: Zebrafish embryos from the transgenic line Tgddx4:ddx4 EGFP on the background of ABTL were injected with the Csm complex targeted against the EGFP transcript or mock solution StCsm buffer without xxx proteins. The RNA was isolated from the pooled embryos at three time points: 128 cell stage  5 hpf and 24 hpf. Three replicates were obtained from each experimental condition and time point. Pair end sequencing was performed on the Illumina NextSeq platform.", null, "pubmed:32833532", null, "Mock 128 Rep 2", "GSM4407862", null, "source name:whole zebrafish embryo|strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:128 cells", "Mock 128 Rep 2", "Base calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. The first 12 nucleotides of read 1  containing the UMI sequence  were extracted and added to the sequence identifier using UMI tools v. 1.0.0. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters:   outFilterType BySJout   outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1   outFilterMismatchNmax 999   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   outFilterMismatchNoverLmax 0.6. Alignments were de duplicated based on their Unique Molecular Identifier sequence using UMI tools v. 1.0.0. De duplicated alignments were counted per exon on the gene level with the htseq count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation. Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package. Genome build: GRCz11 Supplementary files format and content: HTSeq counts.tsv files were generated with htseq count script  they contain counts for each gene for each sample in tab delimited format; normalized counts files were generated with DESeq2  they contain library size normalized read counts for each gene for every sample from each time point in tab delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.", "whole zebrafish embryo", "Zebrafish embryos from three different mating pairs of Tgddx4:ddx4 EGFP females with casper males were pooled during collection. D16A StCsmEGFP was diluted with water for injection 1:1 v/v up to a concentration of 0.7mg/ml. For mock injection  Tris storage buffer 10mM Tris HCl pH8.5  300mM Nacl  1mM DTT  0.1mM EDTA  50% glycerol was also diluted in the similar manner. 1nl of either StCsm EGFP solution 0.7ng or buffer alone were injected into the yolk of embryos at the 1 cell stage. In total  three independent injections were performed. 25 embryos for both StCsm and mock injected per replica set per time point were frozen in liquid nitrogen  stored at xxx\u2103  and processed together.", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer\u2019s protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer\u2019s protocol.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.", "strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:128 cells", "GSM4407862", "GSM4407862: Mock 128 Rep 2; Danio rerio; RNA Seq", "GSM4407862", null, "1", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer's protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer's protocol.", "GEO Accession:GSM4407862", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP252498", null, null, "Mock-128-Rep-2_R1.fastq.gz Mock-128-Rep-2_R2.fastq.gz", "fastq fastq", 3077994140.0, 23676878.0, "GSM4407862 r1", "0:71 1:59", "A:848976357;C:649900868;G:727344485;T:847525958;N:4246472", 71, 59, null, null, 848976357, 649900868, 727344485, 847525958, 4246472, "SRX7899065", "SRS6307321", "SRA1054182", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.56754, 0.4574, 0.03419, 0.02915, 0.77299, 0.78934, 0.5285, 0.53073, 71, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Poland", "2020-03-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [57249, "SRR11293502", "SRX7899064", "SRS6307320", "SRP252498", "PRJNA612134", "Targeted RNA Knockdown by a Type III CRISPR Cas Complex in Zebrafish", "GSE146852", "Transcriptome Analysis", "RNA interference RNAi is a powerful experimental tool for RNA knockdown  but not all organisms are amenable. Here  we provide a \u201cproof of principle\u201d demonstration that CRISPR endoribonuclease can be used for programmable mRNA transcript degradation in eukaryotes. Using zebrafish as the animal model and Csm complex as the CRISPR endoribonuclease  we targeted EGFP transcript expressed from a variety of promoters. A drastic decrease of fluorescence was achieved in germ cells of the vasa:EGFP line. Weaker effects were also seen in fish lines that express EGFP zygotically. Knockdown was statistically significant in cmcl2:EGFP and fli1:EGFP zebrafish lines at 1 dpf dpf  but reduced to background levels at 2 dpf. The nkx2.5:EGFP fish line was least susceptible to Csm mediated EGFP knockdown. We also tested Csm mediated knockdown on the endogenous tdgf1 oep transcript. At optimal Csm dose  we observed a penetrance of the characteristic one eyed phenotype at greater than 50% penetrance  and hence with similar efficiency to morpholino mediated knockdown. We conclude that Csm mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts  in some cases reaching comparable efficiency to morpholino based knockdown with no significant off target effects in our model. Overall design: Zebrafish embryos from the transgenic line Tgddx4:ddx4 EGFP on the background of ABTL were injected with the Csm complex targeted against the EGFP transcript or mock solution StCsm buffer without xxx proteins. The RNA was isolated from the pooled embryos at three time points: 128 cell stage  5 hpf and 24 hpf. Three replicates were obtained from each experimental condition and time point. Pair end sequencing was performed on the Illumina NextSeq platform.", null, "pubmed:32833532", null, "Mock 128 Rep 1", "GSM4407861", null, "source name:whole zebrafish embryo|strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:128 cells", "Mock 128 Rep 1", "Base calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. The first 12 nucleotides of read 1  containing the UMI sequence  were extracted and added to the sequence identifier using UMI tools v. 1.0.0. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters:   outFilterType BySJout   outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1   outFilterMismatchNmax 999   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   outFilterMismatchNoverLmax 0.6. Alignments were de duplicated based on their Unique Molecular Identifier sequence using UMI tools v. 1.0.0. De duplicated alignments were counted per exon on the gene level with the htseq count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation. Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package. Genome build: GRCz11 Supplementary files format and content: HTSeq counts.tsv files were generated with htseq count script  they contain counts for each gene for each sample in tab delimited format; normalized counts files were generated with DESeq2  they contain library size normalized read counts for each gene for every sample from each time point in tab delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.", "whole zebrafish embryo", "Zebrafish embryos from three different mating pairs of Tgddx4:ddx4 EGFP females with casper males were pooled during collection. D16A StCsmEGFP was diluted with water for injection 1:1 v/v up to a concentration of 0.7mg/ml. For mock injection  Tris storage buffer 10mM Tris HCl pH8.5  300mM Nacl  1mM DTT  0.1mM EDTA  50% glycerol was also diluted in the similar manner. 1nl of either StCsm EGFP solution 0.7ng or buffer alone were injected into the yolk of embryos at the 1 cell stage. In total  three independent injections were performed. 25 embryos for both StCsm and mock injected per replica set per time point were frozen in liquid nitrogen  stored at xxx\u2103  and processed together.", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer\u2019s protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer\u2019s protocol.", "Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.", "strain:ABTL Tgddx4:ddx4 EGFP|tissue:whole embryo|condition:Mock|developmental stage:128 cells", "GSM4407861", "GSM4407861: Mock 128 Rep 1; Danio rerio; RNA Seq", "GSM4407861", null, "1", "25 embryos each for both StCsm and mock injected were pooled at xxx cell stage  5 hpf and 24 hpf from xxx biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution Invitrogen according to the manufacturer's protocol. RNA was further purified using Zymo RNA Clean and Concentrator 5 kit according to manufacturer's protocol. 1.5 ug of total RNA was subjected to Lexogen polyA RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA Seq Library Prep Kit according to the Lexogen manufacturer's protocol.", "GEO Accession:GSM4407861", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP252498", null, null, "Mock-128-Rep-1_R1.fastq.gz Mock-128-Rep-1_R2.fastq.gz", "fastq fastq", 2811933150.0, 21630255.0, "GSM4407861 r1", "0:71 1:59", "A:767935312;C:600889090;G:669149820;T:770070432;N:3888496", 71, 59, null, null, 767935312, 600889090, 669149820, 770070432, 3888496, "SRX7899064", "SRS6307320", "SRA1054182", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 2, 0.56804, 0.46336, 0.04038, 0.03346, 0.77638, 0.79032, 0.53645, 0.52653, 71, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Poland", "2020-03-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 151, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", 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