{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and experiment.platform = \"DNBSEQ\"", "rows": [[68685, "SRR18173220", "SRX14320215", "SRS12136321", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "Control 48hpf Replicate 4", "GSM5924083", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "Control 48hpf Replicate 4", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "GSM5924083", "GSM5924083: Control 48hpf Replicate 4; Danio rerio; RNA Seq", "GSM5924083 r1", "GSM5924083", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "Control_48hpf_4_2.fq.gz Control_48hpf_4_1.fq.gz", "fastq fastq", 4893304000.0, 48933040.0, "GSM5924083 r1", "0:100 1:100", "A:1295107147;C:1131453899;G:1158231463;T:1307269653;N:1241838", 100, 100, null, null, 1295107147, 1131453899, 1158231463, 1307269653, 1241838, "SRX14320215", "SRS12136321", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94011, null, 0.0801, null, 0.6927, null, 0.48073, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68686, "SRR18173221", "SRX14320214", "SRS12136320", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "Control 48hpf Replicate 3", "GSM5924082", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "Control 48hpf Replicate 3", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "GSM5924082", "GSM5924082: Control 48hpf Replicate 3; Danio rerio; RNA Seq", "GSM5924082 r1", "GSM5924082", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "Control_48hpf_3_1.fq.gz Control_48hpf_3_2.fq.gz", "fastq fastq", 4673710400.0, 46737104.0, "GSM5924082 r1", "0:100 1:100", "A:1239135128;C:1079263067;G:1106439223;T:1248694558;N:178424", 100, 100, null, null, 1239135128, 1079263067, 1106439223, 1248694558, 178424, "SRX14320214", "SRS12136320", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.9388, null, 0.09027, null, 0.6896, null, 0.47121, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68687, "SRR18173222", "SRX14320213", "SRS12136319", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "Control 48hpf Replicate 2", "GSM5924081", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "Control 48hpf Replicate 2", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "GSM5924081", "GSM5924081: Control 48hpf Replicate 2; Danio rerio; RNA Seq", "GSM5924081 r1", "GSM5924081", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "Control_48hpf_2_2.fq.gz Control_48hpf_2_1.fq.gz", "fastq fastq", 4669056600.0, 46690566.0, "GSM5924081 r1", "0:100 1:100", "A:1230949768;C:1083419632;G:1111527320;T:1243051944;N:107936", 100, 100, null, null, 1230949768, 1083419632, 1111527320, 1243051944, 107936, "SRX14320213", "SRS12136319", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94517, null, 0.08072, null, 0.70084, null, 0.47423, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68688, "SRR18173223", "SRX14320212", "SRS12136318", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "Control 48hpf Replicate 1", "GSM5924080", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "Control 48hpf Replicate 1", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:Control", "GSM5924080", "GSM5924080: Control 48hpf Replicate 1; Danio rerio; RNA Seq", "GSM5924080 r1", "GSM5924080", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "Control_48hpf_1_2.fq.gz Control_48hpf_1_1.fq.gz", "fastq fastq", 4710239800.0, 47102398.0, "GSM5924080 r1", "0:100 1:100", "A:1244163615;C:1092143032;G:1118126753;T:1255696249;N:110151", 100, 100, null, null, 1244163615, 1092143032, 1118126753, 1255696249, 110151, "SRX14320212", "SRS12136318", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94203, null, 0.08895, null, 0.69335, null, 0.46922, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68693, "SRR18173228", "SRX14320207", "SRS12136313", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "5G 48hpf Replicate 4", "GSM5924075", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "5G 48hpf Replicate 4", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "GSM5924075", "GSM5924075: 5G 48hpf Replicate 4; Danio rerio; RNA Seq", "GSM5924075 r1", "GSM5924075", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "5G_48hpf_4_2.fq.gz 5G_48hpf_4_1.fq.gz", "fastq fastq", 3960397600.0, 39603976.0, "GSM5924075 r1", "0:100 1:100", "A:1055375851;C:908722788;G:931610403;T:1063707959;N:980599", 100, 100, null, null, 1055375851, 908722788, 931610403, 1063707959, 980599, "SRX14320207", "SRS12136313", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93498, null, 0.09353, null, 0.6884, null, 0.48205, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68694, "SRR18173229", "SRX14320206", "SRS12136312", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "5G 48hpf Replicate 3", "GSM5924074", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "5G 48hpf Replicate 3", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "GSM5924074", "GSM5924074: 5G 48hpf Replicate 3; Danio rerio; RNA Seq", "GSM5924074 r1", "GSM5924074", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "5G_48hpf_3_1.fq.gz 5G_48hpf_3_2.fq.gz", "fastq fastq", 4666094000.0, 46660940.0, "GSM5924074 r1", "0:100 1:100", "A:1237561088;C:1075964364;G:1103985038;T:1248326386;N:257124", 100, 100, null, null, 1237561088, 1075964364, 1103985038, 1248326386, 257124, "SRX14320206", "SRS12136312", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93689, null, 0.09226, null, 0.68655, null, 0.46431, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68695, "SRR18173230", "SRX14320205", "SRS12136311", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "5G 48hpf Replicate 2", "GSM5924073", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "5G 48hpf Replicate 2", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "GSM5924073", "GSM5924073: 5G 48hpf Replicate 2; Danio rerio; RNA Seq", "GSM5924073 r1", "GSM5924073", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "5G_48hpf_2_1.fq.gz 5G_48hpf_2_2.fq.gz", "fastq fastq", 4687152000.0, 46871520.0, "GSM5924073 r1", "0:100 1:100", "A:1241838266;C:1082317123;G:1110355516;T:1252466907;N:174188", 100, 100, null, null, 1241838266, 1082317123, 1110355516, 1252466907, 174188, "SRX14320205", "SRS12136311", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94454, null, 0.08717, null, 0.69122, null, 0.47277, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [68696, "SRR18173231", "SRX14320204", "SRS12136310", "SRP361858", "PRJNA811237", "Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish", "GSE197627", "Transcriptome Analysis", "Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments   Controls and RFR exposed referred to as \"5G\". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz  30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "pubmed:35434172", null, "5G 48hpf Replicate 1", "GSM5924072", null, "source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "5G 48hpf Replicate 1", "SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.", "Zebrafish embryonic total RNA", "Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "tissue:whole embryos|developmental stage:48 hpf|treatment:5G", "GSM5924072", "GSM5924072: 5G 48hpf Replicate 1; Danio rerio; RNA Seq", "GSM5924072 r1", "GSM5924072", "1", "Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform  with 100 bl PE.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G50", null, "SRP361858", null, null, "5G_48hpf_1_1.fq.gz 5G_48hpf_1_2.fq.gz", "fastq fastq", 4703041000.0, 47030410.0, "GSM5924072 r1", "0:100 1:100", "A:1245130239;C:1085229448;G:1115856477;T:1256653090;N:171746", 100, 100, null, null, 1245130239, 1085229448, 1115856477, 1256653090, 171746, "SRX14320204", "SRS12136310", "SRA1379040", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94571, null, 0.0868, null, 0.69798, null, 0.47971, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-28", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [74329, "SRR23635030", "SRX19518333", "SRS16905710", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 2  bulk RNAseq", "GSM7067524", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 2  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067524", "GSM7067524: KO  replicate 2  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067524 r1", "GSM7067524", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "KO2.fastq.gz", "fastq", 4188284200.0, 41882842.0, "GSM7067524 r1", "0:100", "A:1066992737;C:1011357361;G:1055554148;T:1041284278;N:13095676", 100, null, null, null, 1066992737, 1011357361, 1055554148, 1041284278, 13095676, "SRX19518333", "SRS16905710", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.88647, null, 0.07541, null, 0.7237, null, 0.47069, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74330, "SRR23635031", "SRX19518332", "SRS16905709", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 1  bulk RNAseq", "GSM7067523", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 1  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067523", "GSM7067523: KO  replicate 1  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067523 r1", "GSM7067523", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "KO1.fastq.gz", "fastq", 4181083400.0, 41810834.0, "GSM7067523 r1", "0:100", "A:1077414361;C:996554293;G:1053357384;T:1040649776;N:13107586", 100, null, null, null, 1077414361, 996554293, 1053357384, 1040649776, 13107586, "SRX19518332", "SRS16905709", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.87685, null, 0.07522, null, 0.72699, null, 0.48859, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74331, "SRR23635032", "SRX19518331", "SRS16905708", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 2  bulk RNAseq", "GSM7067522", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 2  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067522", "GSM7067522: WT  replicate 2  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067522 r1", "GSM7067522", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "WT2.fastq.gz", "fastq", 1435167700.0, 14351677.0, "GSM7067522 r1", "0:100", "A:371412640;C:334204906;G:351277070;T:371684263;N:6588821", 100, null, null, null, 371412640, 334204906, 351277070, 371684263, 6588821, "SRX19518331", "SRS16905708", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.83841, null, 0.15087, null, 0.71417, null, 0.50982, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74332, "SRR23635033", "SRX19518330", "SRS16905707", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 1  bulk RNAseq", "GSM7067521", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 1  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067521", "GSM7067521: WT  replicate 1  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067521 r1", "GSM7067521", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "WT1.fastq.gz", "fastq", 1961618800.0, 19616188.0, "GSM7067521 r1", "0:100", "A:518460045;C:447438337;G:477081234;T:509513188;N:9125996", 100, null, null, null, 518460045, 447438337, 477081234, 509513188, 9125996, "SRX19518330", "SRS16905707", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.81315, null, 0.14097, null, 0.72342, null, 0.50905, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 12, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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