run_metadata
20 rows where experiment.library_layout = "PAIRED" and experiment.library_strategy = "ncRNA-Seq"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 49332 | 49332 | SRR7888761 | SRX4726390 | SRS3810123 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 72h | GSM3397729 | source name:Embryo|tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT | 72h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT | GSM3397729 | GSM3397729: 72h; Danio rerio; ncRNA Seq | GSM3397729 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397729 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 72h_1.fq.gz 72h_2.fq.gz | fastq fastq | 12097159200.0 | 40323864.0 | GSM3397729 r1 | 0:150 1:150 | A:2809307023;C:3169515166;G:3184429517;T:2931448896;N:2458598 | 150 | 150 | 2809307023 | 3169515166 | 3184429517 | 2931448896 | 2458598 | SRX4726390 | SRS3810123 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.90426 | 0.90717 | 0.27165 | 0.26439 | 0.70739 | 0.72397 | 0.60155 | 0.60561 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Larval | Larval | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49333 | 49333 | SRR7888760 | SRX4726389 | SRS3810122 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 48h | GSM3397728 | source name:Embryo|tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT | 48h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT | GSM3397728 | GSM3397728: 48h; Danio rerio; ncRNA Seq | GSM3397728 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397728 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 48h_2.fq.gz 48h_1.fq.gz | fastq fastq | 13525174500.0 | 45083915.0 | GSM3397728 r1 | 0:150 1:150 | A:2352542664;C:4312268007;G:4256218842;T:2601416951;N:2728036 | 150 | 150 | 2352542664 | 4312268007 | 4256218842 | 2601416951 | 2728036 | SRX4726389 | SRS3810122 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.91614 | 0.91412 | 0.12891 | 0.12218 | 0.76751 | 0.77948 | 0.71008 | 0.73648 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49334 | 49334 | SRR7888759 | SRX4726388 | SRS3810120 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 24h | GSM3397727 | source name:Embryo|tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT | 24h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT | GSM3397727 | GSM3397727: 24h; Danio rerio; ncRNA Seq | GSM3397727 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397727 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 24h_1.fq.gz 24h_2.fq.gz | fastq fastq | 14333175000.0 | 47777250.0 | GSM3397727 r1 | 0:150 1:150 | A:2728754113;C:4276840070;G:4344116037;T:2980570245;N:2894535 | 150 | 150 | 2728754113 | 4276840070 | 4344116037 | 2980570245 | 2894535 | SRX4726388 | SRS3810120 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.89719 | 0.89478 | 0.18044 | 0.18119 | 0.76942 | 0.7876 | 0.75758 | 0.75366 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49335 | 49335 | SRR7888758 | SRX4726387 | SRS3810121 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 8h | GSM3397726 | source name:Embryo|tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT | 8h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT | GSM3397726 | GSM3397726: 8h; Danio rerio; ncRNA Seq | GSM3397726 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397726 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 8h_2.fq.gz 8h_1.fq.gz | fastq fastq | 15434085600.0 | 51446952.0 | GSM3397726 r1 | 0:150 1:150 | A:2318158791;C:5134519748;G:5292209580;T:2686084369;N:3113112 | 150 | 150 | 2318158791 | 5134519748 | 5292209580 | 2686084369 | 3113112 | SRX4726387 | SRS3810121 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.95788 | 0.95584 | 0.07233 | 0.07686 | 0.81889 | 0.82946 | 0.81383 | 0.80143 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49336 | 49336 | SRR7888757 | SRX4726386 | SRS3810119 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 4.5h | GSM3397725 | source name:Embryo|tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT | 4.5h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT | GSM3397725 | GSM3397725: 4.5h; Danio rerio; ncRNA Seq | GSM3397725 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397725 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 4_5h_2.fq.gz 4_5h_1.fq.gz | fastq fastq | 12988242600.0 | 43294142.0 | GSM3397725 r1 | 0:150 1:150 | A:2232301074;C:3998769528;G:4233380689;T:2521224783;N:2566526 | 150 | 150 | 2232301074 | 3998769528 | 4233380689 | 2521224783 | 2566526 | SRX4726386 | SRS3810119 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.96961 | 0.96817 | 0.05627 | 0.05463 | 0.77068 | 0.78198 | 0.74899 | 0.75759 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 67823 | 67823 | SRR17335719 | SRX13511115 | SRS11405356 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | CPF3 | GSM5754470 | source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing | CPF3 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:CPF toxication | GSM5754470 | GSM5754470: CPF3; Danio rerio; ncRNA Seq | GSM5754470 r1 | GSM5754470 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | CPF3_1.fq.gz CPF3_2.fq.gz | fastq fastq | 12726241500.0 | 42420805.0 | GSM5754470 r1 | 0:150 1:150 | A:3447613023;C:2896153797;G:2922038320;T:3459698412;N:737948 | 150 | 150 | 3447613023 | 2896153797 | 2922038320 | 3459698412 | 737948 | SRX13511115 | SRS11405356 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.89399 | 0.89612 | 0.38172 | 0.37657 | 0.66628 | 0.66799 | 0.53056 | 0.53213 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67824 | 67824 | SRR17335720 | SRX13511114 | SRS11405355 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | CPF2 | GSM5754469 | source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing | CPF2 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:CPF toxication | GSM5754469 | GSM5754469: CPF2; Danio rerio; ncRNA Seq | GSM5754469 r1 | GSM5754469 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | CPF2_1.fq.gz CPF2_2.fq.gz | fastq fastq | 14881715100.0 | 49605717.0 | GSM5754469 r1 | 0:150 1:150 | A:4214905088;C:3201163283;G:3225795074;T:4239665352;N:186303 | 150 | 150 | 4214905088 | 3201163283 | 3225795074 | 4239665352 | 186303 | SRX13511114 | SRS11405355 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.87491 | 0.87638 | 0.40844 | 0.40479 | 0.67123 | 0.67018 | 0.49174 | 0.48952 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67825 | 67825 | SRR17335721 | SRX13511113 | SRS11405354 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | CPF1 | GSM5754468 | source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing | CPF1 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:CPF toxication | GSM5754468 | GSM5754468: CPF1; Danio rerio; ncRNA Seq | GSM5754468 r1 | GSM5754468 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | CPF1_1.fq.gz CPF1_2.fq.gz | fastq fastq | 16447798800.0 | 54825996.0 | GSM5754468 r1 | 0:150 1:150 | A:4454573413;C:3748270411;G:3776995203;T:4467442717;N:517056 | 150 | 150 | 4454573413 | 3748270411 | 3776995203 | 4467442717 | 517056 | SRX13511113 | SRS11405354 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.89313 | 0.8947 | 0.35381 | 0.35194 | 0.64954 | 0.64831 | 0.51962 | 0.52475 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67826 | 67826 | SRR17335722 | SRX13511112 | SRS11405353 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | CYP3 | GSM5754467 | source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing | CYP3 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:CYP toxication | GSM5754467 | GSM5754467: CYP3; Danio rerio; ncRNA Seq | GSM5754467 r1 | GSM5754467 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | CYP3_1.fq.gz CYP3_2.fq.gz | fastq fastq | 13417868100.0 | 44726227.0 | GSM5754467 r1 | 0:150 1:150 | A:3645134270;C:3041754103;G:3084809543;T:3645750889;N:419295 | 150 | 150 | 3645134270 | 3041754103 | 3084809543 | 3645750889 | 419295 | SRX13511112 | SRS11405353 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.86122 | 0.8638 | 0.4112 | 0.40785 | 0.68738 | 0.68519 | 0.54768 | 0.44856 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67827 | 67827 | SRR17335723 | SRX13511111 | SRS11405352 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | CYP2 | GSM5754466 | source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing | CYP2 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:CYP toxication | GSM5754466 | GSM5754466: CYP2; Danio rerio; ncRNA Seq | GSM5754466 r1 | GSM5754466 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | CYP2_1.fq.gz CYP2_2.fq.gz | fastq fastq | 13096007700.0 | 43653359.0 | GSM5754466 r1 | 0:150 1:150 | A:3638241155;C:2892284693;G:2925857490;T:3639296449;N:327913 | 150 | 150 | 3638241155 | 2892284693 | 2925857490 | 3639296449 | 327913 | SRX13511111 | SRS11405352 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.85953 | 0.86247 | 0.41975 | 0.41734 | 0.68174 | 0.67862 | 0.52504 | 0.5324 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67828 | 67828 | SRR17335724 | SRX13511110 | SRS11405351 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | CYP1 | GSM5754465 | source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing | CYP1 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:CYP toxication | GSM5754465 | GSM5754465: CYP1; Danio rerio; ncRNA Seq | GSM5754465 r1 | GSM5754465 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | CYP1_1.fq.gz CYP1_2.fq.gz | fastq fastq | 16372872000.0 | 54576240.0 | GSM5754465 r1 | 0:150 1:150 | A:4747286217;C:3417115980;G:3453793026;T:4754530080;N:146697 | 150 | 150 | 4747286217 | 3417115980 | 3453793026 | 4754530080 | 146697 | SRX13511110 | SRS11405351 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.85322 | 0.85414 | 0.46298 | 0.45901 | 0.68016 | 0.67866 | 0.47694 | 0.47897 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67829 | 67829 | SRR17335725 | SRX13511109 | SRS11405350 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | Cont3 | GSM5754464 | source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing | Cont3 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:No toxication | GSM5754464 | GSM5754464: Cont3; Danio rerio; ncRNA Seq | GSM5754464 r1 | GSM5754464 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | Cont3_1.fq.gz Cont3_2.fq.gz | fastq fastq | 15202443900.0 | 50674813.0 | GSM5754464 r1 | 0:150 1:150 | A:4400470018;C:3173803928;G:3218623722;T:4409335756;N:210476 | 150 | 150 | 4400470018 | 3173803928 | 3218623722 | 4409335756 | 210476 | SRX13511109 | SRS11405350 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.86129 | 0.84677 | 0.45657 | 0.44799 | 0.67884 | 0.68083 | 0.48291 | 0.4763 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67830 | 67830 | SRR17335726 | SRX13511108 | SRS11405349 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | Cont2 | GSM5754463 | source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing | Cont2 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:No toxication | GSM5754463 | GSM5754463: Cont2; Danio rerio; ncRNA Seq | GSM5754463 r1 | GSM5754463 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | Cont2_1.fq.gz Cont2_2.fq.gz | fastq fastq | 12927267600.0 | 43090892.0 | GSM5754463 r1 | 0:150 1:150 | A:3474574877;C:2959326086;G:3006553706;T:3486600752;N:212179 | 150 | 150 | 3474574877 | 2959326086 | 3006553706 | 3486600752 | 212179 | SRX13511108 | SRS11405349 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.87695 | 0.87907 | 0.41673 | 0.41416 | 0.69266 | 0.69266 | 0.53339 | 0.58145 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 67831 | 67831 | SRR17335727 | SRX13511107 | SRS11405348 | SRP352585 | PRJNA792582 | circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio | GSE192669 | Transcriptome Analysis | Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish | pubmed:35304207 | Cont1 | GSM5754462 | source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing | Cont1 | Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes … | Brain tissue | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Brain|treatment:No toxication | GSM5754462 | GSM5754462: Cont1; Danio rerio; ncRNA Seq | GSM5754462 r1 | GSM5754462 | 1 | Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352585 | loader:fastq load.py | Cont1_1.fq.gz Cont1_2.fq.gz | fastq fastq | 18395362500.0 | 61317875.0 | GSM5754462 r1 | 0:150 1:150 | A:5379624768;C:3792463355;G:3842313235;T:5380702187;N:258955 | 150 | 150 | 5379624768 | 3792463355 | 3842313235 | 5380702187 | 258955 | SRX13511107 | SRS11405348 | SRA1349262 | Atatürk University | Atatürk University | 2 | 0.83439 | 0.83446 | 0.45703 | 0.44894 | 0.68828 | 0.68578 | 0.4957 | 0.49639 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Turkey | 2021-12-27 | Undetermined | Undetermined | Brain | Nervous System | |||||||||||
| 68556 | 68556 | SRR18028171 | SRX14182301 | SRS12005942 | SRP359829 | PRJNA807002 | samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf | PRJNA807002 | Other | In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway. | 6WT 3 | strain:AB|isolate:replicate3|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal | wt 3 S11 L001 R1 | 011 | 011 | Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing. | ncRNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | HiSeq X Ten | SRP359829 | wt-3_S11_L001_R1_001.fastq.gz wt-3_S11_L001_R2_001.fastq.gz | fastq fastq | 3576981600.0 | 11923272.0 | wt 3 S11 L001 R1 001.fastq.gz | 0:150 1:150 | A:689001630;C:496844981;G:1779990511;T:610974133;N:170345 | 150 | 150 | 689001630 | 496844981 | 1779990511 | 610974133 | 170345 | SRX14182301 | SRS12005942 | SRA1372890 | Huazhong agricultural university|School of Life Science and Technology | Huazhong agricultural university | 2 | 0.8179 | 0.81697 | 0.60905 | 0.60864 | 0.82692 | 0.82915 | 0.52425 | 0.52623 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | China | 2022-02-14 | Multi-stage | Multi-stage | Gonad | Reproductive System | |||||||||||||||||||||
| 68557 | 68557 | SRR18028172 | SRX14182300 | SRS12005941 | SRP359829 | PRJNA807002 | samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf | PRJNA807002 | Other | In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway. | 5WT 2 | strain:AB|isolate:replicate2|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal | wt 2 S10 L001 R1 | 009 | 009 | Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing. | ncRNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | HiSeq X Ten | SRP359829 | wt-2_S10_L001_R1_001.fastq.gz wt-2_S10_L001_R2_001.fastq.gz | fastq fastq | 4200013800.0 | 14000046.0 | wt 2 S10 L001 R1 001.fastq.gz | 0:150 1:150 | A:781057232;C:617020885;G:2110010128;T:691723797;N:201758 | 150 | 150 | 781057232 | 617020885 | 2110010128 | 691723797 | 201758 | SRX14182300 | SRS12005941 | SRA1372890 | Huazhong agricultural university|School of Life Science and Technology | Huazhong agricultural university | 2 | 0.8213 | 0.82216 | 0.59414 | 0.59507 | 0.81089 | 0.81306 | 0.53839 | 0.52755 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | China | 2022-02-14 | Multi-stage | Multi-stage | Gonad | Reproductive System | |||||||||||||||||||||
| 68558 | 68558 | SRR18028173 | SRX14182299 | SRS12005940 | SRP359829 | PRJNA807002 | samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf | PRJNA807002 | Other | In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway. | 4WT 1 | strain:AB|isolate:replicate1|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal | wt 1 S9 L001 R1 | 007 | 007 | Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing. | ncRNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | HiSeq X Ten | SRP359829 | wt-1_S9_L001_R1_001.fastq.gz wt-1_S9_L001_R2_001.fastq.gz | fastq fastq | 4820063700.0 | 16066879.0 | wt 1 S9 L001 R1 001.fastq.gz | 0:150 1:150 | A:996304548;C:657334691;G:2379519106;T:786675131;N:230224 | 150 | 150 | 996304548 | 657334691 | 2379519106 | 786675131 | 230224 | SRX14182299 | SRS12005940 | SRA1372890 | Huazhong agricultural university|School of Life Science and Technology | Huazhong agricultural university | 2 | 0.80219 | 0.80319 | 0.60906 | 0.60878 | 0.83238 | 0.83303 | 0.52559 | 0.51852 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | China | 2022-02-14 | Multi-stage | Multi-stage | Gonad | Reproductive System | |||||||||||||||||||||
| 68559 | 68559 | SRR18028174 | SRX14182298 | SRS12005939 | SRP359829 | PRJNA807002 | samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf | PRJNA807002 | Other | In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway. | 3PLD6 3 | strain:AB|isolate:replicate3|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal | pld6 3 S3 L003 R1 | 005 | 005 | Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing. | ncRNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | HiSeq X Ten | SRP359829 | pld6-3_S3_L003_R1_001.fastq.gz pld6-3_S3_L003_R2_001.fastq.gz | fastq fastq | 816686700.0 | 2722289.0 | pld6 3 S3 L003 R1 001.fastq.gz | 0:150 1:150 | A:145681738;C:137123477;G:401610833;T:132256312;N:14340 | 150 | 150 | 145681738 | 137123477 | 401610833 | 132256312 | 14340 | SRX14182298 | SRS12005939 | SRA1372890 | Huazhong agricultural university|School of Life Science and Technology | Huazhong agricultural university | 2 | 0.78314 | 0.73942 | 0.07641 | 0.09097 | 0.91603 | 0.91545 | 0.6312 | 0.64467 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | China | 2022-02-14 | Multi-stage | Multi-stage | Gonad | Reproductive System | |||||||||||||||||||||
| 68560 | 68560 | SRR18028175 | SRX14182297 | SRS12005938 | SRP359829 | PRJNA807002 | samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf | PRJNA807002 | Other | In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway. | 2PLD6 2 | strain:AB|isolate:replicate2|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal | pld6 2 S2 L003 R1 | 003 | 003 | Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing. | ncRNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | HiSeq X Ten | SRP359829 | pld6-2_S2_L003_R1_001.fastq.gz pld6-2_S2_L003_R2_001.fastq.gz | fastq fastq | 6546276900.0 | 21820923.0 | pld6 2 S2 L003 R1 001.fastq.gz | 0:150 1:150 | A:1161502458;C:1095580994;G:3226725392;T:1062358099;N:109957 | 150 | 150 | 1161502458 | 1095580994 | 3226725392 | 1062358099 | 109957 | SRX14182297 | SRS12005938 | SRA1372890 | Huazhong agricultural university|School of Life Science and Technology | Huazhong agricultural university | 2 | 0.6471 | 0.593 | 0.07935 | 0.09168 | 0.92058 | 0.92005 | 0.53626 | 0.65284 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | China | 2022-02-14 | Multi-stage | Multi-stage | Gonad | Reproductive System | |||||||||||||||||||||
| 68561 | 68561 | SRR18028176 | SRX14182296 | SRS12005937 | SRP359829 | PRJNA807002 | samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf | PRJNA807002 | Other | In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway. | 1PLD6 1 | strain:AB|isolate:replicate1|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal | pld6 1 S1 L003 R1 | 001 | 001 | Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing. | ncRNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | HiSeq X Ten | SRP359829 | pld6-1_S1_L003_R1_001.fastq.gz pld6-1_S1_L003_R2_001.fastq.gz | fastq fastq | 5535130200.0 | 18450434.0 | pld6 1 S1 L003 R1 001.fastq.gz | 0:150 1:150 | A:1014761790;C:833992394;G:2813863824;T:872418512;N:93680 | 150 | 150 | 1014761790 | 833992394 | 2813863824 | 872418512 | 93680 | SRX14182296 | SRS12005937 | SRA1372890 | Huazhong agricultural university|School of Life Science and Technology | Huazhong agricultural university | 2 | 0.70358 | 0.73288 | 0.08649 | 0.09366 | 0.91066 | 0.90914 | 0.6197 | 0.6207 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | China | 2022-02-14 | Multi-stage | Multi-stage | Gonad | Reproductive System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;