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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1230", null, "library ID:H 3|title:High 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "High 3", "H 3", "H 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz", "fastq fastq", 6117817800.0, 20392726.0, "S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz", "0:150 1:150", "A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211", 150, 150, null, null, 1635728688, 1405168032, 1464072107, 1612834762, 14211, "SRX23704452", "SRS20534448", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30659, "SRR28054754", "SRX23704451", "SRS20534446", "SRP491086", "PRJNA1078753", "Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1229", null, "library ID:H 2|title:High 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1229 rep1 1 URNA S73 L003 R1 001.fastq|filename2:S21K1229 rep1 1 URNA S73 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "High 2", "H 2", "H 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1229_rep1_1_URNA_S73_L003_R1_001.fastq.gz S21K1229_rep1_1_URNA_S73_L003_R2_001.fastq.gz", "fastq fastq", 7164803100.0, 23882677.0, "S21K1229 rep1 1 URNA S73 L003 R1 001.fastq.gz", "0:150 1:150", "A:1920286881;C:1649856655;G:1697032084;T:1897610671;N:16809", 150, 150, null, null, 1920286881, 1649856655, 1697032084, 1897610671, 16809, "SRX23704451", "SRS20534446", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30660, "SRR28054755", "SRX23704450", "SRS20534445", "SRP491086", "PRJNA1078753", "Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1220", null, "library ID:C 2|title:Control 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1220 rep1 1 URNA S64 L003 R1 001.fastq|filename2:S21K1220 rep1 1 URNA S64 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control 2", "C 2", "C 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1220_rep1_1_URNA_S64_L003_R1_001.fastq.gz S21K1220_rep1_1_URNA_S64_L003_R2_001.fastq.gz", "fastq fastq", 6790504800.0, 22635016.0, "S21K1220 rep1 1 URNA S64 L003 R1 001.fastq.gz", "0:150 1:150", "A:1784553430;C:1593393319;G:1650087761;T:1762454671;N:15619", 150, 150, null, null, 1784553430, 1593393319, 1650087761, 1762454671, 15619, "SRX23704450", "SRS20534445", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30661, "SRR28054756", "SRX23704449", "SRS20534444", "SRP491086", "PRJNA1078753", "Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1219", null, "library ID:C 1|title:Control 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1219 rep1 1 URNA S63 L003 R1 001.fastq|filename2:S21K1219 rep1 1 URNA S63 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control 1", "C 1", "C 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1219_rep1_1_URNA_S63_L003_R1_001.fastq.gz S21K1219_rep1_1_URNA_S63_L003_R2_001.fastq.gz", "fastq fastq", 7498264200.0, 24994214.0, "S21K1219 rep1 1 URNA S63 L003 R1 001.fastq.gz", "0:150 1:150", "A:2002773492;C:1716996682;G:1800329295;T:1978147319;N:17412", 150, 150, null, null, 2002773492, 1716996682, 1800329295, 1978147319, 17412, "SRX23704449", "SRS20534444", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30662, "SRR28125659", "SRX23770350", "SRS20595835", "SRP492124", "PRJNA1081449", "Thymic mimetic cells in zebrafish", "GSE259418", "Transcriptome Analysis", "We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult Thymus 2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile Thymus 1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile Thymus 2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile Thymus 3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile Thymus 4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5", null, null, null, "adult thy untreated", "GSM8115869", null, "tissue:13 wpf wpf loc name:missing|collection date:missing", "adult thy untreated", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms", "13 wpf", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "tissue:13 wpf", "GSM8115869", "GSM8115869: adult thy untreated; Danio rerio; RNA Seq", "GSM8115869 r1", "GSM8115869", "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP492124", null, "loader:fastq load.py", "adult_thy_untreated_S5_L001_R2_001.fastq.gz adult_thy_untreated_S5_L001_R1_001.fastq.gz adult_thy_untreated_S5_L001_I1_001.fastq.gz", "fastq fastq fastq", 61867658967.0, 487146921.0, "GSM8115869 r1", "0:8 1:28 2:91", "A:12933400034;C:9373762639;G:10188374364;T:11834295354;N:537420", 8, 28, 91, null, 12933400034, 9373762639, 10188374364, 11834295354, 537420, "SRX23770350", "SRS20595835", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.90847, null, 0.19603, null, 0.76895, null, 0.56494, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-27", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [30663, "SRR28125660", "SRX23770349", "SRS20595836", "SRP492124", "PRJNA1081449", "Thymic mimetic cells in zebrafish", "GSE259418", "Transcriptome Analysis", "We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult Thymus 2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile Thymus 1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile Thymus 2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile Thymus 3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile Thymus 4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5", null, null, null, "adult thy liberase 2", "GSM8115868", null, "tissue:13 wpf wpf loc name:missing|collection date:missing", "adult thy liberase 2", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms", "13 wpf", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "tissue:13 wpf", "GSM8115868", "GSM8115868: adult thy liberase 2; Danio rerio; RNA Seq", "GSM8115868 r1", "GSM8115868", "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP492124", null, "loader:fastq load.py", "adult_thy_liberase_2_S7_L001_I1_001.fastq.gz adult_thy_liberase_2_S7_L001_R1_001.fastq.gz adult_thy_liberase_2_S7_L001_R2_001.fastq.gz", "fastq fastq fastq", 64816880653.0, 510369139.0, "GSM8115868 r1", "0:8 1:28 2:91", "A:12985717325;C:10400471721;G:10926930853;T:12129907262;N:564488", 8, 28, 91, null, 12985717325, 10400471721, 10926930853, 12129907262, 564488, "SRX23770349", "SRS20595836", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.90014, null, 0.13619, null, 0.81103, null, 0.54906, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-27", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [30664, "SRR28125661", "SRX23770348", "SRS20595834", "SRP492124", "PRJNA1081449", "Thymic mimetic cells in zebrafish", "GSE259418", "Transcriptome Analysis", "We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult Thymus 2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile Thymus 1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile Thymus 2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile Thymus 3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile Thymus 4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5", null, null, null, "adult thy liberase 1", "GSM8115867", null, "tissue:13 wpf wpf loc name:missing|collection date:missing", "adult thy liberase 1", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms", "13 wpf", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "tissue:13 wpf", "GSM8115867", "GSM8115867: adult thy liberase 1; Danio rerio; RNA Seq", "GSM8115867 r1", "GSM8115867", "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP492124", null, "loader:fastq load.py", "adult_thy_liberase_1_S6_L001_I1_001.fastq.gz adult_thy_liberase_1_S6_L001_R1_001.fastq.gz adult_thy_liberase_1_S6_L001_R2_001.fastq.gz", "fastq fastq fastq", 62862684917.0, 494981771.0, "GSM8115867 r1", "0:8 1:28 2:91", "A:12631971877;C:10077821577;G:10579831603;T:11753169367;N:546737", 8, 28, 91, null, 12631971877, 10077821577, 10579831603, 11753169367, 546737, "SRX23770348", "SRS20595834", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.89921, null, 0.13602, null, 0.814, null, 0.55224, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-27", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37961, "SRR1205174", "SRX501301", "SRS582373", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 5hr 3", "GSM1357182", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "cntl neo 5hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "GSM1357182", "GSM1357182: cntl neo 5hr 3; Danio rerio; RNA Seq", "GSM1357182", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357182", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_5_3.fastq.gz", "fastq", 1630216750.0, 32604335.0, "GSM1357182 r1", "0:50 1:0", "A:435441738;C:384703554;G:377838654;T:432163463;N:69341", 50, 0, null, null, 435441738, 384703554, 377838654, 432163463, 69341, "SRX501301", "SRS582373", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93632, null, 0.20492, null, 0.67551, null, 0.50281, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37962, "SRR1205173", "SRX501300", "SRS582372", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 5hr 2", "GSM1357181", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "cntl neo 5hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "GSM1357181", "GSM1357181: cntl neo 5hr 2; Danio rerio; RNA Seq", "GSM1357181", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357181", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_5_2.fastq.gz", "fastq", 1812797550.0, 36255951.0, "GSM1357181 r1", "0:50 1:0", "A:484800524;C:426109547;G:417833682;T:483968870;N:84927", 50, 0, null, null, 484800524, 426109547, 417833682, 483968870, 84927, "SRX501300", "SRS582372", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93602, null, 0.21513, null, 0.67517, null, 0.49404, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37963, "SRR1205172", "SRX501299", "SRS582371", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 5hr 1", "GSM1357180", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "cntl neo 5hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "GSM1357180", "GSM1357180: cntl neo 5hr 1; Danio rerio; RNA Seq", "GSM1357180", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357180", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_5_1.fastq.gz", "fastq", 1616736500.0, 32334730.0, "GSM1357180 r1", "0:50 1:0", "A:425328931;C:388105733;G:379129548;T:424100489;N:71799", 50, 0, null, null, 425328931, 388105733, 379129548, 424100489, 71799, "SRX501299", "SRS582371", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.9361, null, 0.23516, null, 0.68091, null, 0.50961, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37964, "SRR1205171", "SRX501298", "SRS582370", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 5hr 3", "GSM1357179", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "gfp neo 5hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "GSM1357179", "GSM1357179: gfp neo 5hr 3; Danio rerio; RNA Seq", "GSM1357179", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357179", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_5_3.fastq.gz", "fastq", 1856512100.0, 37130242.0, "GSM1357179 r1", "0:50 1:0", "A:492227117;C:440944515;G:431529818;T:491731276;N:79374", 50, 0, null, null, 492227117, 440944515, 431529818, 491731276, 79374, "SRX501298", "SRS582370", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93677, null, 0.28732, null, 0.71435, null, 0.50496, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37965, "SRR1205170", "SRX501297", "SRS582369", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 5hr 2", "GSM1357178", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "gfp neo 5hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "GSM1357178", "GSM1357178: gfp neo 5hr 2; Danio rerio; RNA Seq", "GSM1357178", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357178", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_5_2.fastq.gz", "fastq", 1605154400.0, 32103088.0, "GSM1357178 r1", "0:50 1:0", "A:431076570;C:373656204;G:367046732;T:433299718;N:75176", 50, 0, null, null, 431076570, 373656204, 367046732, 433299718, 75176, "SRX501297", "SRS582369", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93022, null, 0.29198, null, 0.69656, null, 0.47675, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37966, "SRR1205169", "SRX501296", "SRS582368", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 5hr 1", "GSM1357177", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "gfp neo 5hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "GSM1357177", "GSM1357177: gfp neo 5hr 1; Danio rerio; RNA Seq", "GSM1357177", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357177", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_5_1.fastq.gz", "fastq", 1902899900.0, 38057998.0, "GSM1357177 r1", "0:50 1:0", "A:511489376;C:443148505;G:433716076;T:514461324;N:84619", 50, 0, null, null, 511489376, 443148505, 433716076, 514461324, 84619, "SRX501296", "SRS582368", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.92977, null, 0.29647, null, 0.69583, null, 0.48582, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37967, "SRR1205168", "SRX501295", "SRS582367", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 3hr 3", "GSM1357176", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "cntl neo 3hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "GSM1357176", "GSM1357176: cntl neo 3hr 3; Danio rerio; RNA Seq", "GSM1357176", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357176", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_3_3.fastq.gz", "fastq", 1555198750.0, 31103975.0, "GSM1357176 r1", "0:50 1:0", "A:416734314;C:365733903;G:359113904;T:413549150;N:67479", 50, 0, null, null, 416734314, 365733903, 359113904, 413549150, 67479, "SRX501295", "SRS582367", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93432, null, 0.21789, null, 0.67363, null, 0.49063, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37968, "SRR1205167", "SRX501294", "SRS582366", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 3hr 2", "GSM1357175", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "cntl neo 3hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "GSM1357175", "GSM1357175: cntl neo 3hr 2; Danio rerio; RNA Seq", "GSM1357175", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357175", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_3_2.fastq.gz", "fastq", 1701011300.0, 34020226.0, "GSM1357175 r1", "0:50 1:0", "A:453767169;C:401144167;G:392795706;T:453224665;N:79593", 50, 0, null, null, 453767169, 401144167, 392795706, 453224665, 79593, "SRX501294", "SRS582366", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93437, null, 0.19214, null, 0.66884, null, 0.48995, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37969, "SRR1205166", "SRX501293", "SRS582365", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 3hr 1", "GSM1357174", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "cntl neo 3hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012", "GSM1357174", "GSM1357174: cntl neo 3hr 1; Danio rerio; RNA Seq", "GSM1357174", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357174", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_3_1.fastq.gz", "fastq", 1228792200.0, 24575844.0, "GSM1357174 r1", "0:50 1:0", "A:328509222;C:288306723;G:283185002;T:328736353;N:54900", 50, 0, null, null, 328509222, 288306723, 283185002, 328736353, 54900, "SRX501293", "SRS582365", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93269, null, 0.21003, null, 0.66592, null, 0.48875, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37970, "SRR1205165", "SRX501292", "SRS582364", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 3hr 3", "GSM1357173", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "gfp neo 3hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "GSM1357173", "GSM1357173: gfp neo 3hr 3; Danio rerio; RNA Seq", "GSM1357173", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357173", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_3_3.fastq.gz", "fastq", 1406657700.0, 28133154.0, "GSM1357173 r1", "0:50 1:0", "A:379997165;C:326224852;G:320555458;T:379818406;N:61819", 50, 0, null, null, 379997165, 326224852, 320555458, 379818406, 61819, "SRX501292", "SRS582364", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.9327, null, 0.3167, null, 0.70709, null, 0.48722, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37971, "SRR1205164", "SRX501291", "SRS582363", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 3hr 2", "GSM1357172", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "gfp neo 3hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "GSM1357172", "GSM1357172: gfp neo 3hr 2; Danio rerio; RNA Seq", "GSM1357172", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357172", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_3_2.fastq.gz", "fastq", 1409177900.0, 28183558.0, "GSM1357172 r1", "0:50 1:0", "A:377366991;C:329654609;G:322942817;T:379147506;N:65977", 50, 0, null, null, 377366991, 329654609, 322942817, 379147506, 65977, "SRX501291", "SRS582363", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.92559, null, 0.27573, null, 0.69968, null, 0.48668, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37972, "SRR1205163", "SRX501290", "SRS582362", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 3hr 1", "GSM1357171", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "gfp neo 3hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012", "GSM1357171", "GSM1357171: gfp neo 3hr 1; Danio rerio; RNA Seq", "GSM1357171", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357171", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_3_1.fastq.gz", "fastq", 1364255100.0, 27285102.0, "GSM1357171 r1", "0:50 1:0", "A:367031933;C:317262942;G:311363762;T:368536308;N:60155", 50, 0, null, null, 367031933, 317262942, 311363762, 368536308, 60155, "SRX501290", "SRS582362", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93433, null, 0.34822, null, 0.70504, null, 0.49052, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37973, "SRR1205162", "SRX501289", "SRS582361", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp nt 1hr 3", "GSM1357170", null, "tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "gfp nt 1hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "GSM1357170", "GSM1357170: gfp nt 1hr 3; Danio rerio; RNA Seq", "GSM1357170", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357170", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_nt_1_3.fastq.gz", "fastq", 2032585500.0, 40651710.0, "GSM1357170 r1", "0:50 1:0", "A:540423336;C:478257444;G:470055372;T:543729414;N:119934", 50, 0, null, null, 540423336, 478257444, 470055372, 543729414, 119934, "SRX501289", "SRS582361", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93511, null, 0.2696, null, 0.70425, null, 0.49291, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37974, "SRR1205161", "SRX501288", "SRS582360", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp nt 1hr 2", "GSM1357169", null, "tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "gfp nt 1hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "GSM1357169", "GSM1357169: gfp nt 1hr 2; Danio rerio; RNA Seq", "GSM1357169", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357169", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_nt_1_2.fastq.gz", "fastq", 1562346650.0, 31246933.0, "GSM1357169 r1", "0:50 1:0", "A:414164641;C:369142355;G:361974997;T:416978503;N:86154", 50, 0, null, null, 414164641, 369142355, 361974997, 416978503, 86154, "SRX501288", "SRS582360", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93897, null, 0.31695, null, 0.70991, null, 0.50448, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37975, "SRR1205160", "SRX501287", "SRS582359", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp nt 1hr 1", "GSM1357168", null, "tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "gfp nt 1hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "GSM1357168", "GSM1357168: gfp nt 1hr 1; Danio rerio; RNA Seq", "GSM1357168", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357168", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_nt_1_1.fastq.gz", "fastq", 1689050050.0, 33781001.0, "GSM1357168 r1", "0:50 1:0", "A:453271567;C:394505701;G:386090706;T:455068897;N:113179", 50, 0, null, null, 453271567, 394505701, 386090706, 455068897, 113179, "SRX501287", "SRS582359", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93627, null, 0.28408, null, 0.70585, null, 0.48065, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37976, "SRR1205159", "SRX501286", "SRS582358", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 1hr 3", "GSM1357167", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "gfp neo 1hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "GSM1357167", "GSM1357167: gfp neo 1hr 3; Danio rerio; RNA Seq", "GSM1357167", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357167", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_1_3.fastq.gz", "fastq", 1611919200.0, 32238384.0, "GSM1357167 r1", "0:50 1:0", "A:428150047;C:380113504;G:372605259;T:430955158;N:95232", 50, 0, null, null, 428150047, 380113504, 372605259, 430955158, 95232, "SRX501286", "SRS582358", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.94024, null, 0.31287, null, 0.71601, null, 0.50103, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37977, "SRR1205158", "SRX501285", "SRS582357", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 1hr 2", "GSM1357166", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "gfp neo 1hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "GSM1357166", "GSM1357166: gfp neo 1hr 2; Danio rerio; RNA Seq", "GSM1357166", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357166", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_1_2.fastq.gz", "fastq", 1653679950.0, 33073599.0, "GSM1357166 r1", "0:50 1:0", "A:439492851;C:388625865;G:381772828;T:443698911;N:89495", 50, 0, null, null, 439492851, 388625865, 381772828, 443698911, 89495, "SRX501285", "SRS582357", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.94345, null, 0.38847, null, 0.7357, null, 0.50373, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37978, "SRR1205157", "SRX501284", "SRS582356", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "gfp neo 1hr 1", "GSM1357165", null, "tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "gfp neo 1hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP positive cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012", "GSM1357165", "GSM1357165: gfp neo 1hr 1; Danio rerio; RNA Seq", "GSM1357165", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357165", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "gfp_neo_1_1.fastq.gz", "fastq", 1873022200.0, 37460444.0, "GSM1357165 r1", "0:50 1:0", "A:501397145;C:438845045;G:428481612;T:504171995;N:126403", 50, 0, null, null, 501397145, 438845045, 428481612, 504171995, 126403, "SRX501284", "SRS582356", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.933, null, 0.24769, null, 0.70591, null, 0.50587, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37979, "SRR1205156", "SRX501283", "SRS582355", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl nt 1hr 3", "GSM1357164", null, "tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "cntl nt 1hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "GSM1357164", "GSM1357164: cntl nt 1hr 3; Danio rerio; RNA Seq", "GSM1357164", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357164", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_nt_1_3.fastq.gz", "fastq", 1523970250.0, 30479405.0, "GSM1357164 r1", "0:50 1:0", "A:404458518;C:360948466;G:353690676;T:404782977;N:89613", 50, 0, null, null, 404458518, 360948466, 353690676, 404782977, 89613, "SRX501283", "SRS582355", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93995, null, 0.21232, null, 0.66772, null, 0.48499, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37980, "SRR1205155", "SRX501282", "SRS582354", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl nt 1hr 2", "GSM1357163", null, "tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "cntl nt 1hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "GSM1357163", "GSM1357163: cntl nt 1hr 2; Danio rerio; RNA Seq", "GSM1357163", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357163", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_nt_1_2.fastq.gz", "fastq", 1649622150.0, 32992443.0, "GSM1357163 r1", "0:50 1:0", "A:434980357;C:392949654;G:385359402;T:436242531;N:90206", 50, 0, null, null, 434980357, 392949654, 385359402, 436242531, 90206, "SRX501282", "SRS582354", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.94128, null, 0.24395, null, 0.67549, null, 0.50787, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37981, "SRR1205154", "SRX501281", "SRS582353", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl nt 1hr 1", "GSM1357162", null, "tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "cntl nt 1hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "GSM1357162", "GSM1357162: cntl nt 1hr 1; Danio rerio; RNA Seq", "GSM1357162", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357162", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_nt_1_1.fastq.gz", "fastq", 1953710600.0, 39074212.0, "GSM1357162 r1", "0:50 1:0", "A:518489677;C:462970545;G:452495723;T:519623507;N:131148", 50, 0, null, null, 518489677, 462970545, 452495723, 519623507, 131148, "SRX501281", "SRS582353", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93818, null, 0.2175, null, 0.66229, null, 0.50468, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37982, "SRR1205153", "SRX501280", "SRS582352", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 1hr 3", "GSM1357161", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "cntl neo 1hr 3", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "GSM1357161", "GSM1357161: cntl neo 1hr 3; Danio rerio; RNA Seq", "GSM1357161", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_1_3.fastq.gz", "fastq", 1934085200.0, 38681704.0, "GSM1357161 r1", "0:50 1:0", "A:513203802;C:458221455;G:449581302;T:512967391;N:111250", 50, 0, null, null, 513203802, 458221455, 449581302, 512967391, 111250, "SRX501280", "SRS582352", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93811, null, 0.22613, null, 0.66671, null, 0.49681, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37983, "SRR1205152", "SRX501279", "SRS582351", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 1hr 2", "GSM1357160", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "cntl neo 1hr 2", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "GSM1357160", "GSM1357160: cntl neo 1hr 2; Danio rerio; RNA Seq", "GSM1357160", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357160", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_1_2.fastq.gz", "fastq", 1836127900.0, 36722558.0, "GSM1357160 r1", "0:50 1:0", "A:485828745;C:436091545;G:426562682;T:487543575;N:101353", 50, 0, null, null, 485828745, 436091545, 426562682, 487543575, 101353, "SRX501279", "SRS582351", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93856, null, 0.23223, null, 0.67154, null, 0.5021, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [37984, "SRR1205151", "SRX501278", "SRS582350", "SRP040561", "PRJNA242641", "Gene expression analysis of hair cell regeneration in the zebrafish lateral line", "GSE56176", "Transcriptome Analysis", "Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.", null, "pubmed:24706903", null, "cntl neo 1hr 1", "GSM1357159", null, "tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "cntl neo 1hr 1", "Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options \u2013g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.", "GFP negative cells from 5 dpf larvae", "For neomycin treatment 5dpf larvae were treated for 30min with 300\u03bcM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5\u00b0C for the indicated time.", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5\u00b0C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.", "drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012", "GSM1357159", "GSM1357159: cntl neo 1hr 1; Danio rerio; RNA Seq", "GSM1357159", null, "1", "Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer\u2019s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.", "GEO Accession:GSM1357159", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP040561", null, "loader:latf load", "cntl_neo_1_1.fastq.gz", "fastq", 1687481850.0, 33749637.0, "GSM1357159 r1", "0:50 1:0", "A:448529802;C:398804686;G:391019451;T:449013498;N:114413", 50, 0, null, null, 448529802, 398804686, 391019451, 449013498, 114413, "SRX501278", "SRS582350", "SRA149178", "GEO", "Seidel, Genomics, Stowers Institute", 1, 0.93698, null, 0.21557, null, 0.66436, null, 0.49756, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-03-25", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [43465, "SRR6888838", "SRX3839388", "SRS3086676", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 WKM Scar", "GSM3065994", null, "tissue:WKM single cells|cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "P2 WKM Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "WKM single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "GSM3065994", "GSM3065994: P2 WKM Scar; Danio rerio; RNA Seq", "GSM3065994", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-WKM-001-Scar_R1.fastq.gz P2-WKM-001-Scar_R2.fastq.gz", "fastq fastq", 344288293.0, 2265619.0, "GSM3065994 r1", "0:75.98 1:75.98", "A:60840077;C:100295730;G:126071444;T:57044397;N:36645", 75, 75, null, null, 60840077, 100295730, 126071444, 57044397, 36645, "SRX3839388", "SRS3086676", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0007, 0.00458, 0.00047, 0.00268, 0.99971, 0.99669, 0.37837, 0.42452, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [43466, "SRR6888839", "SRX3839388", "SRS3086676", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 WKM Scar", "GSM3065994", null, "tissue:WKM single cells|cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "P2 WKM Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "WKM single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "GSM3065994", "GSM3065994: P2 WKM Scar; Danio rerio; RNA Seq", "GSM3065994", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-WKM-002-Scar_R1.fastq.gz P2-WKM-002-Scar_R2.fastq.gz", "fastq fastq", 717066879.0, 4719933.0, "GSM3065994 r2", "0:75.98 1:75.94", "A:126563252;C:209265530;G:262732780;T:118432095;N:73222", 75, 75, null, null, 126563252, 209265530, 262732780, 118432095, 73222, "SRX3839388", "SRS3086676", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00063, 0.1196, 0.00034, 0.0666, 0.99977, 0.99598, 0.23529, 0.45161, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [63586, "SRR13951240", "SRX10330055", "SRS8449856", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT acrolein treated rep6", "GSM5169491", null, "source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae", "Zebrafish larvae WT acrolein treated rep6", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT acrolein treated larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Acrolein|tissue:Larvae", "GSM5169491", "GSM5169491: Zebrafish larvae WT acrolein treated rep6; Danio rerio; RNA Seq", "GSM5169491", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169491", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAALRAAPEI-515_1.fq.gz V300079388_L3_HK500ZEBaopEAALRAAPEI-515_2.fq.gz", "fastq fastq", 4980022200.0, 49800222.0, "GSM5169491 r1", "0:100 1:100", "A:1333773139;C:1140685596;G:1152592074;T:1352971391;N:0", 100, 100, null, null, 1333773139, 1140685596, 1152592074, 1352971391, 0, "SRX10330055", "SRS8449856", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.9486, null, 0.11229, null, 0.65967, null, 0.47337, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63587, "SRR13951239", "SRX10330054", "SRS8449858", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT acrolein treated rep5", "GSM5169490", null, "source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae", "Zebrafish larvae WT acrolein treated rep5", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT acrolein treated larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Acrolein|tissue:Larvae", "GSM5169490", "GSM5169490: Zebrafish larvae WT acrolein treated rep5; Danio rerio; RNA Seq", "GSM5169490", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169490", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_1.fq.gz V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_2.fq.gz", "fastq fastq", 4989256800.0, 49892568.0, "GSM5169490 r1", "0:100 1:100", "A:1333967860;C:1145275940;G:1156212626;T:1353800374;N:0", 100, 100, null, null, 1333967860, 1145275940, 1156212626, 1353800374, 0, "SRX10330054", "SRS8449858", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94949, null, 0.10728, null, 0.65756, null, 0.47006, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63588, "SRR13951238", "SRX10330053", "SRS8449857", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT acrolein treated rep4", "GSM5169489", null, "source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae", "Zebrafish larvae WT acrolein treated rep4", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT acrolein treated larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Acrolein|tissue:Larvae", "GSM5169489", "GSM5169489: Zebrafish larvae WT acrolein treated rep4; Danio rerio; RNA Seq", "GSM5169489", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169489", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_1.fq.gz V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_2.fq.gz", "fastq fastq", 4991600600.0, 49916006.0, "GSM5169489 r1", "0:100 1:100", "A:1332160517;C:1148004219;G:1159807037;T:1351628827;N:0", 100, 100, null, null, 1332160517, 1148004219, 1159807037, 1351628827, 0, "SRX10330053", "SRS8449857", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.95038, null, 0.10485, null, 0.65977, null, 0.47668, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63589, "SRR13951237", "SRX10330052", "SRS8449855", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT acrolein treated rep3", "GSM5169488", null, "source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae", "Zebrafish larvae WT acrolein treated rep3", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT acrolein treated larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Acrolein|tissue:Larvae", "GSM5169488", "GSM5169488: Zebrafish larvae WT acrolein treated rep3; Danio rerio; RNA Seq", "GSM5169488", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169488", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_1.fq.gz V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_2.fq.gz", "fastq fastq", 4931029800.0, 49310298.0, "GSM5169488 r1", "0:100 1:100", "A:1313566945;C:1137259809;G:1149091650;T:1331111396;N:0", 100, 100, null, null, 1313566945, 1137259809, 1149091650, 1331111396, 0, "SRX10330052", "SRS8449855", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.95011, null, 0.10594, null, 0.65711, null, 0.48179, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63590, "SRR13951236", "SRX10330051", "SRS8449854", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT acrolein treated rep2", "GSM5169487", null, "source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae", "Zebrafish larvae WT acrolein treated rep2", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT acrolein treated larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Acrolein|tissue:Larvae", "GSM5169487", "GSM5169487: Zebrafish larvae WT acrolein treated rep2; Danio rerio; RNA Seq", "GSM5169487", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169487", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_1.fq.gz V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_2.fq.gz", "fastq fastq", 4934978600.0, 49349786.0, "GSM5169487 r1", "0:100 1:100", "A:1318738318;C:1133208442;G:1143616038;T:1339415802;N:0", 100, 100, null, null, 1318738318, 1133208442, 1143616038, 1339415802, 0, "SRX10330051", "SRS8449854", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.948, null, 0.10568, null, 0.65685, null, 0.45325, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63591, "SRR13951235", "SRX10330050", "SRS8449851", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT acrolein treated rep1", "GSM5169486", null, "source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae", "Zebrafish larvae WT acrolein treated rep1", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT acrolein treated larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Acrolein|tissue:Larvae", "GSM5169486", "GSM5169486: Zebrafish larvae WT acrolein treated rep1; Danio rerio; RNA Seq", "GSM5169486", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169486", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_1.fq.gz V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_2.fq.gz", "fastq fastq", 4916868000.0, 49168680.0, "GSM5169486 r1", "0:100 1:100", "A:1319311116;C:1122812867;G:1129767432;T:1344976585;N:0", 100, 100, null, null, 1319311116, 1122812867, 1129767432, 1344976585, 0, "SRX10330050", "SRS8449851", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94789, null, 0.10769, null, 0.65537, null, 0.47629, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63592, "SRR13951234", "SRX10330049", "SRS8449853", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT rep6", "GSM5169485", null, "source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae WT rep6", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Ctrl|tissue:Larvae", "GSM5169485", "GSM5169485: Zebrafish larvae WT rep6; Danio rerio; RNA Seq", "GSM5169485", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169485", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_1.fq.gz V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_2.fq.gz", "fastq fastq", 4918223600.0, 49182236.0, "GSM5169485 r1", "0:100 1:100", "A:1312501446;C:1129859893;G:1141743360;T:1334118901;N:0", 100, 100, null, null, 1312501446, 1129859893, 1141743360, 1334118901, 0, "SRX10330049", "SRS8449853", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94736, null, 0.10854, null, 0.66095, null, 0.46684, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63593, "SRR13951251", "SRX10330048", "SRS8449849", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT rep5", "GSM5169484", null, "source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae WT rep5", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Ctrl|tissue:Larvae", "GSM5169484", "GSM5169484: Zebrafish larvae WT rep5; Danio rerio; RNA Seq", "GSM5169484", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169484", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAAERAAPEI-505_1.fq.gz V300079388_L2_HK500ZEBaopEAAERAAPEI-505_2.fq.gz", "fastq fastq", 4921487400.0, 49214874.0, "GSM5169484 r1", "0:100 1:100", "A:1307773420;C:1137100007;G:1147334476;T:1329279497;N:0", 100, 100, null, null, 1307773420, 1137100007, 1147334476, 1329279497, 0, "SRX10330048", "SRS8449849", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.9488, null, 0.10243, null, 0.65596, null, 0.47526, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63594, "SRR13951250", "SRX10330047", "SRS8449847", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT rep4", "GSM5169483", null, "source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae WT rep4", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Ctrl|tissue:Larvae", "GSM5169483", "GSM5169483: Zebrafish larvae WT rep4; Danio rerio; RNA Seq", "GSM5169483", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169483", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAADRAAPEI-504_1.fq.gz V300079388_L2_HK500ZEBaopEAADRAAPEI-504_2.fq.gz", "fastq fastq", 4902200200.0, 49022002.0, "GSM5169483 r1", "0:100 1:100", "A:1302490426;C:1131663107;G:1148042501;T:1320004166;N:0", 100, 100, null, null, 1302490426, 1131663107, 1148042501, 1320004166, 0, "SRX10330047", "SRS8449847", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.9486, null, 0.10416, null, 0.66133, null, 0.45959, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63595, "SRR13951249", "SRX10330046", "SRS8449846", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT rep3", "GSM5169482", null, "source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae WT rep3", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Ctrl|tissue:Larvae", "GSM5169482", "GSM5169482: Zebrafish larvae WT rep3; Danio rerio; RNA Seq", "GSM5169482", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169482", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAACRAAPEI-503_1.fq.gz V300079388_L2_HK500ZEBaopEAACRAAPEI-503_2.fq.gz", "fastq fastq", 4932506000.0, 49325060.0, "GSM5169482 r1", "0:100 1:100", "A:1314021251;C:1136250372;G:1148046464;T:1334187913;N:0", 100, 100, null, null, 1314021251, 1136250372, 1148046464, 1334187913, 0, "SRX10330046", "SRS8449846", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.95001, null, 0.10334, null, 0.66003, null, 0.474, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63596, "SRR13951248", "SRX10330045", "SRS8449848", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT rep2", "GSM5169481", null, "source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae WT rep2", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Ctrl|tissue:Larvae", "GSM5169481", "GSM5169481: Zebrafish larvae WT rep2; Danio rerio; RNA Seq", "GSM5169481", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169481", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAABRAAPEI-502_1.fq.gz V300079388_L2_HK500ZEBaopEAABRAAPEI-502_2.fq.gz", "fastq fastq", 4938494000.0, 49384940.0, "GSM5169481 r1", "0:100 1:100", "A:1313976068;C:1139517379;G:1153604159;T:1331396394;N:0", 100, 100, null, null, 1313976068, 1139517379, 1153604159, 1331396394, 0, "SRX10330045", "SRS8449848", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94864, null, 0.10252, null, 0.65957, null, 0.47642, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63597, "SRR13951247", "SRX10330044", "SRS8449845", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae WT rep1", "GSM5169480", null, "source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae WT rep1", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae WT larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:WT|treatment:Ctrl|tissue:Larvae", "GSM5169480", "GSM5169480: Zebrafish larvae WT rep1; Danio rerio; RNA Seq", "GSM5169480", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169480", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L2_HK500ZEBaopEAAARAAPEI-501_1.fq.gz V300079388_L2_HK500ZEBaopEAAARAAPEI-501_2.fq.gz", "fastq fastq", 4920498800.0, 49204988.0, "GSM5169480 r1", "0:100 1:100", "A:1312070030;C:1133298664;G:1141858537;T:1333271569;N:0", 100, 100, null, null, 1312070030, 1133298664, 1141858537, 1333271569, 0, "SRX10330044", "SRS8449845", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94865, null, 0.10459, null, 0.65965, null, 0.46788, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63598, "SRR13951246", "SRX10330043", "SRS8449844", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep6", "GSM5169479", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep6", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169479", "GSM5169479: Zebrafish larvae akr1a1a KO rep6; Danio rerio; RNA Seq", "GSM5169479", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169479", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAARRAAPEI-521_1.fq.gz V300079388_L3_HK500ZEBaopEAARRAAPEI-521_2.fq.gz", "fastq fastq", 4983441000.0, 49834410.0, "GSM5169479 r1", "0:100 1:100", "A:1322739180;C:1153664354;G:1168919194;T:1338118272;N:0", 100, 100, null, null, 1322739180, 1153664354, 1168919194, 1338118272, 0, "SRX10330043", "SRS8449844", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.9473, null, 0.09632, null, 0.66419, null, 0.46649, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63599, "SRR13951245", "SRX10330042", "SRS8449843", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep5", "GSM5169478", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep5", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169478", "GSM5169478: Zebrafish larvae akr1a1a KO rep5; Danio rerio; RNA Seq", "GSM5169478", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169478", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_1.fq.gz V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_2.fq.gz", "fastq fastq", 4979727600.0, 49797276.0, "GSM5169478 r1", "0:100 1:100", "A:1324141918;C:1150666829;G:1165518713;T:1339400140;N:0", 100, 100, null, null, 1324141918, 1150666829, 1165518713, 1339400140, 0, "SRX10330042", "SRS8449843", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94914, null, 0.09649, null, 0.66377, null, 0.47093, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63600, "SRR13951244", "SRX10330041", "SRS8449852", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep4", "GSM5169477", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep4", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169477", "GSM5169477: Zebrafish larvae akr1a1a KO rep4; Danio rerio; RNA Seq", "GSM5169477", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169477", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_1.fq.gz V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_2.fq.gz", "fastq fastq", 4978998800.0, 49789988.0, "GSM5169477 r1", "0:100 1:100", "A:1333355936;C:1140285632;G:1151126213;T:1354231019;N:0", 100, 100, null, null, 1333355936, 1140285632, 1151126213, 1354231019, 0, "SRX10330041", "SRS8449852", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94594, null, 0.10032, null, 0.66194, null, 0.48009, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63601, "SRR13951243", "SRX10330040", "SRS8449842", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep3", "GSM5169476", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep3", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169476", "GSM5169476: Zebrafish larvae akr1a1a KO rep3; Danio rerio; RNA Seq", "GSM5169476", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169476", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAORAAPEI-518_1.fq.gz V300079388_L3_HK500ZEBaopEAAORAAPEI-518_2.fq.gz", "fastq fastq", 4978639200.0, 49786392.0, "GSM5169476 r1", "0:100 1:100", "A:1331238273;C:1143633964;G:1152228372;T:1351538591;N:0", 100, 100, null, null, 1331238273, 1143633964, 1152228372, 1351538591, 0, "SRX10330040", "SRS8449842", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94616, null, 0.1007, null, 0.66054, null, 0.46712, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63602, "SRR13951242", "SRX10330039", "SRS8449850", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep2", "GSM5169475", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep2", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169475", "GSM5169475: Zebrafish larvae akr1a1a KO rep2; Danio rerio; RNA Seq", "GSM5169475", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169475", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAANRAAPEI-517_1.fq.gz V300079388_L3_HK500ZEBaopEAANRAAPEI-517_2.fq.gz", "fastq fastq", 4967553600.0, 49675536.0, "GSM5169475 r1", "0:100 1:100", "A:1324408005;C:1143569026;G:1158003192;T:1341573377;N:0", 100, 100, null, null, 1324408005, 1143569026, 1158003192, 1341573377, 0, "SRX10330039", "SRS8449850", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94688, null, 0.09559, null, 0.66158, null, 0.4794, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [63603, "SRR13951241", "SRX10330038", "SRS8449841", "SRP310389", "PRJNA713989", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes", "GSE168786", "Transcriptome Analysis", "Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf", null, "pubmed:34278746;pubmed:36711148", null, "Zebrafish larvae akr1a1a KO rep1", "GSM5169474", null, "source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "Zebrafish larvae akr1a1a KO rep1", "trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "Zebrafish larvae akr1a1a KO larvae", "6 replicates were treated with acrolein from 24 hpf to 120 hpf", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Larvae were kept in E3 media at 28.5\u25e6C with 10% PTU to suppress pigmentation formation.", "genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae", "GSM5169474", "GSM5169474: Zebrafish larvae akr1a1a KO rep1; Danio rerio; RNA Seq", "GSM5169474", null, "1", "Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5169474", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP310389", null, null, "V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_1.fq.gz V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_2.fq.gz", "fastq fastq", 4967500800.0, 49675008.0, "GSM5169474 r1", "0:100 1:100", "A:1323753410;C:1144795675;G:1158403216;T:1340548499;N:0", 100, 100, null, null, 1323753410, 1144795675, 1158403216, 1340548499, 0, "SRX10330038", "SRS8449841", "SRA1205863", "GEO", "ZMF, University Heidelberg", 1, 0.94765, null, 0.09715, null, 0.66018, null, 0.4542, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-03-12", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"], [70042, "SRR19364727", "SRX15423206", "SRS13146622", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "BaP eggs 4 RNA seq", "GSM6180938", null, "source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "BaP eggs 4 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "BaP eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "GSM6180938", "GSM6180938: BaP eggs 4 RNA seq; Danio rerio; RNA Seq", "GSM6180938 r1", "GSM6180938", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP376709", null, "loader:fastq load.py", "BaP_eggs_8_R1.fastq.gz BaP_eggs_8_R2.fastq.gz", "fastq fastq", 19115420100.0, 63718067.0, "GSM6180938 r1", "0:150 1:150", "A:4851825995;C:4609263506;G:4922433150;T:4730809159;N:1088290", 150, 150, null, null, 4851825995, 4609263506, 4922433150, 4730809159, 1088290, "SRX15423206", "SRS13146622", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94488, 0.93103, 0.10568, 0.10357, 0.73748, 0.73957, 0.48933, 0.48151, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70043, "SRR19364732", "SRX15423205", "SRS13146621", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "BaP eggs 3 RNA seq", "GSM6180937", null, "source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "BaP eggs 3 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "BaP eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "GSM6180937", "GSM6180937: BaP eggs 3 RNA seq; Danio rerio; RNA Seq", "GSM6180937 r1", "GSM6180937", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP376709", null, "loader:fastq load.py", "BaP_eggs_7_R1.fastq.gz BaP_eggs_7_R2.fastq.gz", "fastq fastq", 19465596300.0, 64885321.0, "GSM6180937 r1", "0:150 1:150", "A:4900471856;C:4741543326;G:5043578096;T:4778894378;N:1108644", 150, 150, null, null, 4900471856, 4741543326, 5043578096, 4778894378, 1108644, "SRX15423205", "SRS13146621", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93506, 0.92058, 0.122, 0.11917, 0.74326, 0.74474, 0.56012, 0.56276, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70044, "SRR19364728", "SRX15423204", "SRS13146620", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "BaP eggs 2 RNA seq", "GSM6180936", null, "source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "BaP eggs 2 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "BaP eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "GSM6180936", "GSM6180936: BaP eggs 2 RNA seq; Danio rerio; RNA Seq", "GSM6180936 r1", "GSM6180936", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP376709", null, "loader:fastq load.py", "BaP_eggs_6_R1.fastq.gz BaP_eggs_6_R2.fastq.gz", "fastq fastq", 26226106500.0, 87420355.0, "GSM6180936 r1", "0:150 1:150", "A:6626146699;C:6360908364;G:6776635828;T:6460933487;N:1482122", 150, 150, null, null, 6626146699, 6360908364, 6776635828, 6460933487, 1482122, "SRX15423204", "SRS13146620", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94617, 0.93149, 0.11317, 0.11079, 0.74054, 0.74263, 0.55952, 0.55897, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70045, "SRR19364731", "SRX15423203", "SRS13146619", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "BaP eggs 1 RNA seq", "GSM6180935", null, "source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "BaP eggs 1 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "BaP eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene", "GSM6180935", "GSM6180935: BaP eggs 1 RNA seq; Danio rerio; RNA Seq", "GSM6180935 r1", "GSM6180935", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP376709", null, "loader:fastq load.py", "BaP_eggs_5_R1.fastq.gz BaP_eggs_5_R2.fastq.gz", "fastq fastq", 18086447700.0, 60288159.0, "GSM6180935 r1", "0:150 1:150", "A:4571847785;C:4383836533;G:4677889533;T:4451843797;N:1030052", 150, 150, null, null, 4571847785, 4383836533, 4677889533, 4451843797, 1030052, "SRX15423203", "SRS13146619", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.9432, 0.92614, 0.11892, 0.11711, 0.73815, 0.74, 0.54654, 0.54731, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70046, "SRR19364729", "SRX15423202", "SRS13146618", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "control eggs 4 RNA seq", "GSM6180934", null, "source name:control eggs|strain:5D|tissue:Eggs|treatment:Control", "control eggs 4 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "control eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Control", "GSM6180934", "GSM6180934: control eggs 4 RNA seq; Danio rerio; RNA Seq", "GSM6180934 r1", "GSM6180934", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "Control_eggs_4_R1.fastq.gz Control_eggs_4_R2.fastq.gz", "fastq fastq", 19391871000.0, 64639570.0, "GSM6180934 r1", "0:150 1:150", "A:4939089340;C:4665115719;G:4975360720;T:4811207801;N:1097420", 150, 150, null, null, 4939089340, 4665115719, 4975360720, 4811207801, 1097420, "SRX15423202", "SRS13146618", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.90666, 0.88778, 0.11871, 0.11531, 0.74578, 0.74795, 0.53529, 0.5334, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70047, "SRR19364730", "SRX15423201", "SRS13146617", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "control eggs 3 RNA seq", "GSM6180933", null, "source name:control eggs|strain:5D|tissue:Eggs|treatment:Control", "control eggs 3 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "control eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Control", "GSM6180933", "GSM6180933: control eggs 3 RNA seq; Danio rerio; RNA Seq", "GSM6180933 r1", "GSM6180933", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "Control_eggs_3_R1.fastq.gz Control_eggs_3_R2.fastq.gz", "fastq fastq", 17489942700.0, 58299809.0, "GSM6180933 r1", "0:150 1:150", "A:4443405922;C:4213832030;G:4502075354;T:4329638793;N:990601", 150, 150, null, null, 4443405922, 4213832030, 4502075354, 4329638793, 990601, "SRX15423201", "SRS13146617", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.9475, 0.93055, 0.10441, 0.10172, 0.74085, 0.74343, 0.56917, 0.571, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70048, "SRR19364733", "SRX15423200", "SRS13146616", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "control eggs 2 RNA seq", "GSM6180932", null, "source name:control eggs|strain:5D|tissue:Eggs|treatment:Control", "control eggs 2 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "control eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Control", "GSM6180932", "GSM6180932: control eggs 2 RNA seq; Danio rerio; RNA Seq", "GSM6180932 r1", "GSM6180932", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "Control_eggs_2_R1.fastq.gz Control_eggs_2_R2.fastq.gz", "fastq fastq", 19848063900.0, 66160213.0, "GSM6180932 r1", "0:150 1:150", "A:5033909827;C:4791850093;G:5120951365;T:4900231037;N:1121578", 150, 150, null, null, 5033909827, 4791850093, 5120951365, 4900231037, 1121578, "SRX15423200", "SRS13146616", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94254, 0.92598, 0.11605, 0.11324, 0.74199, 0.74442, 0.56003, 0.49676, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [70049, "SRR19364734", "SRX15423199", "SRS13146615", "SRP376709", "PRJNA841653", "Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation", "GSE203631", "Other", "Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 \u00b5g/g fish equivalent to 1250 \u00b5g/g food respectively TetraMin\u00ae Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28\u00b0C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.", null, null, null, "control eggs 1 RNA seq", "GSM6180931", null, "source name:control eggs|strain:5D|tissue:Eggs|treatment:Control", "control eggs 1 RNA seq", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.", "control eggs", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.\u00a0 DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:Eggs|treatment:Control", "GSM6180931", "GSM6180931: control eggs 1 RNA seq; Danio rerio; RNA Seq", "GSM6180931 r1", "GSM6180931", "1", "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "Control_eggs_1_R1.fastq.gz Control_eggs_1_R2.fastq.gz", "fastq fastq", 19334898300.0, 64449661.0, "GSM6180931 r1", "0:150 1:150", "A:4874809508;C:4709685650;G:5004647639;T:4744672338;N:1083165", 150, 150, null, null, 4874809508, 4709685650, 5004647639, 4744672338, 1083165, "SRX15423199", "SRS13146615", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93357, 0.91807, 0.10685, 0.10558, 0.73801, 0.74065, 0.5458, 0.54625, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"]], "truncated": false, "filtered_table_rows_count": 67, "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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