{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and experiment.platform = \"ION_TORRENT\"", "rows": [[41410, "SRR4423126", "SRX2245310", "SRS1745848", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 8 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:22 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: 22 somite stage20 hpf", "347 8", "347 8", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S08large.fastq", "fastq", 436406791.0, 4063942.0, "S08large.fastq", "0:107.39", "A:101104674;C:116028113;G:134686941;T:84587063;N:0", 107, null, null, null, 101104674, 116028113, 134686941, 84587063, 0, "SRX2245310", "SRS1745848", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.93717, null, 0.24651, null, 0.93933, null, 0.83386, null, 120, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41411, "SRR4423125", "SRX2245309", "SRS1745849", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 7 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:12 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: 12 somite stage15 hpf", "347 7", "347 7", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S07large.fastq", "fastq", 537626793.0, 4843104.0, "S07large.fastq", "0:111.01", "A:126939058;C:142383462;G:163136732;T:105167541;N:0", 111, null, null, null, 126939058, 142383462, 163136732, 105167541, 0, "SRX2245309", "SRS1745849", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.9417, null, 0.29157, null, 0.93488, null, 0.84573, null, 122, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41412, "SRR4423124", "SRX2245308", "SRS1745856", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 6 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:4 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: 4 somite stage11.3 hpf", "347 6", "347 6", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S06large.fastq", "fastq", 442838850.0, 4133196.0, "S06large.fastq", "0:107.14", "A:102648557;C:119062787;G:133773678;T:87353828;N:0", 107, null, null, null, 102648557, 119062787, 133773678, 87353828, 0, "SRX2245308", "SRS1745856", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.92856, null, 0.24819, null, 0.92622, null, 0.85191, null, 53, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-14", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41429, "SRR4423107", "SRX2245291", "SRS1745856", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 6 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:4 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 4 somite stage11.3 hpf", "348 6", "348 6", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S06small.fastq", "fastq", 535288776.0, 4443685.0, "S06small.fastq", "0:120.46", "A:119322177;C:152704452;G:149509408;T:113752739;N:0", 120, null, null, null, 119322177, 152704452, 149509408, 113752739, 0, "SRX2245291", "SRS1745856", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.82872, null, 0.09035, null, 0.93194, null, 0.81296, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41436, "SRR4423100", "SRX2245284", "SRS1745849", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 7 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:12 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 12 somite stage15 hpf", "348 7", "348 7", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S07small.fastq", "fastq", 279201769.0, 2713759.0, "S07small.fastq", "0:102.88", "A:61655863;C:78667355;G:77702440;T:61176111;N:0", 102, null, null, null, 61655863, 78667355, 77702440, 61176111, 0, "SRX2245284", "SRS1745849", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.79087, null, 0.10046, null, 0.89221, null, 0.77892, null, 158, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41437, "SRR4423099", "SRX2245283", "SRS1745848", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 8 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:22 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 22 somite stage20 hpf", "348 8", "348 8", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S08small.fastq", "fastq", 520785540.0, 4495080.0, "S08small.fastq", "0:115.86", "A:115224831;C:149325753;G:144978190;T:111256766;N:0", 115, null, null, null, 115224831, 149325753, 144978190, 111256766, 0, "SRX2245283", "SRS1745848", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.83781, null, 0.08976, null, 0.92904, null, 0.80492, null, 183, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59506, "SRR11924315", "SRX8469989", "SRS6770640", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "12 somite 3", "GSM4591057", null, "source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "12 somite 3", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "12 somite stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591057", "GSM4591057: 12 somite 3; Danio rerio; OTHER", "GSM4591057", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591057", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "12_somite_3.bam GSE151797_Reference_sequence.fa", "bam bam", 105146264.0, 3189309.0, "GSM4591057 r1", "0:32.97", "A:24684898;C:33906144;G:26247070;T:20308152;N:0", 32, null, null, null, 24684898, 33906144, 26247070, 20308152, 0, "SRX8469989", "SRS6770640", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.83304, null, 0.22816, null, 0.88325, null, 0.69597, null, 43, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Segmentation", "Embryo", "Undetermined", "Embryo Imprecise"], [59507, "SRR11924314", "SRX8469988", "SRS6770639", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "12 somite 2", "GSM4591056", null, "source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "12 somite 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "12 somite stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591056", "GSM4591056: 12 somite 2; Danio rerio; OTHER", "GSM4591056", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591056", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "12_somite_2.bam GSE151797_Reference_sequence.fa", "bam bam", 255844263.0, 7971494.0, "GSM4591056 r1", "0:32.09", "A:53703561;C:85057062;G:64342817;T:52740823;N:0", 32, null, null, null, 53703561, 85057062, 64342817, 52740823, 0, "SRX8469988", "SRS6770639", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.79601, null, 0.23342, null, 0.90281, null, 0.75464, null, 40, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Segmentation", "Embryo", "Undetermined", "Embryo Imprecise"], [59508, "SRR11924312", "SRX8469987", "SRS6770638", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "12 somite 1", "GSM4591055", null, "source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "12 somite 1", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "12 somite stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591055", "GSM4591055: 12 somite 1; Danio rerio; OTHER", "GSM4591055", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591055", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "12_somite_1.bam GSE151797_Reference_sequence.fa", "bam bam", 254000103.0, 7990851.0, "GSM4591055 r1", "0:31.79", "A:52359510;C:82090735;G:62850013;T:56699845;N:0", 31, null, null, null, 52359510, 82090735, 62850013, 56699845, 0, "SRX8469987", "SRS6770638", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.69554, null, 0.21063, null, 0.88284, null, 0.72326, null, 43, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Segmentation", "Embryo", "Undetermined", "Embryo Imprecise"], [62959, "SRR13520382", "SRX9931400", "SRS8106885", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "G8 12: pEGFP N1 injected at 12hpf", "GSM5033117", null, "source name:zebrafish embryos|strain:TU|developmental stage:12hpf|tissue:embryo", "G8 12: pEGFP N1 injected at 12hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:12hpf|tissue:embryo", "GSM5033117", "GSM5033117: G8 12: pEGFP N1 injected at 12hpf; Danio rerio; RNA Seq", "GSM5033117", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "G8-12.fastq.gz", "fastq", 2163053937.0, 12776614.0, "GSM5033117 r1", "0:169.30", "A:581602408;C:540446105;G:566494100;T:474511324;N:0", 169, null, null, null, 581602408, 540446105, 566494100, 474511324, 0, "SRX9931400", "SRS8106885", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.73901, null, 0.01942, null, 0.7726, null, 0.47694, null, 169, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62962, "SRR13520379", "SRX9931397", "SRS8106882", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "C12: un injected at 12hpf", "GSM5033114", null, "source name:zebrafish embryos|strain:TU|developmental stage:12hpf|tissue:embryo", "C12: un injected at 12hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:12hpf|tissue:embryo", "GSM5033114", "GSM5033114: C12: un injected at 12hpf; Danio rerio; RNA Seq", "GSM5033114", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "C12.fastq.gz", "fastq", 2287177824.0, 14569411.0, "GSM5033114 r1", "0:156.98", "A:618744606;C:567027488;G:600125143;T:501280587;N:0", 156, null, null, null, 618744606, 567027488, 600125143, 501280587, 0, "SRX9931397", "SRS8106882", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.74656, null, 0.02098, null, 0.76928, null, 0.47392, null, 184, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 11, "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", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Segmentation", "p1": "ION_TORRENT"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_strategy=OTHER", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "cDNA", "label": "cDNA", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_selection=cDNA", "selected": false}, {"value": "other", "label": "other", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_selection=other", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "Embryo", "label": "Embryo", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "Segmentation", "label": "Segmentation", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ION_TORRENT", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&tissue_curation_coarse=Embryo+Imprecise", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&tissue_curation=Undetermined", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT", "results": [{"value": "unknown", "label": "unknown", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&experiment.platform=ION_TORRENT&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 103.32348400152114}