{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\", technology = \"bulk\" and tissue_curation_coarse = \"Nervous System\"", "rows": [[68382, "SRR17720609", "SRX13883476", "SRS11752245", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Normoxia IP", "GSM5832287", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832287", "GSM5832287: m7G Normoxia IP; Danio rerio; OTHER", "GSM5832287 r1", "GSM5832287", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  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RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Normoxia Input", "GSM5832286", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832286", "GSM5832286: m7G Normoxia Input; Danio rerio; OTHER", "GSM5832286 r1", "GSM5832286", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  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RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Hypoxia IP", "GSM5832285", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832285", "GSM5832285: m7G Hypoxia IP; Danio rerio; OTHER", "GSM5832285 r1", "GSM5832285", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  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RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Hypoxia Input", "GSM5832284", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832284", "GSM5832284: m7G Hypoxia Input; Danio rerio; OTHER", "GSM5832284 r1", "GSM5832284", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  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RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Normoxia IP", "GSM5832283", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832283", "GSM5832283: m6A Normoxia IP; Danio rerio; OTHER", "GSM5832283 r1", "GSM5832283", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, null, "m6A_Normoxia_IP_R1.fastq.gz m6A_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6583667700.0, 21945559.0, "GSM5832283 r1", "0:150 1:150", "A:1750230540;C:1500991424;G:1592129260;T:1740287575;N:28901", 150, 150, null, null, 1750230540, 1500991424, 1592129260, 1740287575, 28901, "SRX13883472", "SRS11752242", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87682, 0.87986, 0.18203, 0.17239, 0.74671, 0.7472, 0.55638, 0.55861, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68387, "SRR17720614", "SRX13883471", "SRS11752240", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Normoxia Input", "GSM5832282", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832282", "GSM5832282: m6A Normoxia Input; Danio rerio; OTHER", "GSM5832282 r1", "GSM5832282", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m6A_Normoxia_Input_R1.fastq.gz m6A_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6314076000.0, 21046920.0, "GSM5832282 r1", "0:150 1:150", "A:1815907910;C:1329572814;G:1378464668;T:1790102301;N:28307", 150, 150, null, null, 1815907910, 1329572814, 1378464668, 1790102301, 28307, "SRX13883471", "SRS11752240", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.91754, 0.91835, 0.21273, 0.20993, 0.69702, 0.69625, 0.53456, 0.53763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68388, "SRR17720615", "SRX13883470", "SRS11752239", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Hypoxia IP", "GSM5832281", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832281", "GSM5832281: m6A Hypoxia IP; Danio rerio; OTHER", "GSM5832281 r1", "GSM5832281", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, null, "m6A_Hypoxia_IP_R1.fastq.gz m6A_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 6490349100.0, 21634497.0, "GSM5832281 r1", "0:150 1:150", "A:1714144102;C:1483635762;G:1606044832;T:1686496024;N:28380", 150, 150, null, null, 1714144102, 1483635762, 1606044832, 1686496024, 28380, "SRX13883470", "SRS11752239", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87598, 0.88161, 0.16783, 0.16105, 0.74588, 0.74568, 0.55361, 0.55307, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68389, "SRR17720616", "SRX13883469", "SRS11752237", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Hypoxia Input", "GSM5832280", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832280", "GSM5832280: m6A Hypoxia Input; Danio rerio; OTHER", "GSM5832280 r1", "GSM5832280", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m6A_Hypoxia_Input_R1.fastq.gz m6A_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 7054483800.0, 23514946.0, "GSM5832280 r1", "0:150 1:150", "A:2000164754;C:1513377207;G:1570441784;T:1970468107;N:31948", 150, 150, null, null, 2000164754, 1513377207, 1570441784, 1970468107, 31948, "SRX13883469", "SRS11752237", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.91916, 0.91997, 0.21403, 0.21158, 0.69716, 0.69503, 0.52616, 0.51982, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68390, "SRR17720617", "SRX13883468", "SRS11752238", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Normoxia IP", "GSM5832279", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832279", "GSM5832279: m5C Normoxia IP; Danio rerio; OTHER", "GSM5832279 r1", "GSM5832279", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Normoxia_IP_R1.fastq.gz m5C_Normoxia_IP_R2.fastq.gz", "fastq fastq", 7385723100.0, 24619077.0, "GSM5832279 r1", "0:150 1:150", "A:1779838658;C:1853060139;G:2010257354;T:1742536078;N:30871", 150, 150, null, null, 1779838658, 1853060139, 2010257354, 1742536078, 30871, "SRX13883468", "SRS11752238", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.88617, 0.87633, 0.42619, 0.41974, 0.71792, 0.74016, 0.69827, 0.68649, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68391, "SRR17720618", "SRX13883467", "SRS11752236", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Normoxia Input", "GSM5832278", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832278", "GSM5832278: m5C Normoxia Input; Danio rerio; OTHER", "GSM5832278 r1", "GSM5832278", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Normoxia_Input_R1.fastq.gz m5C_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6594811500.0, 21982705.0, "GSM5832278 r1", "0:150 1:150", "A:1941068575;C:1341378672;G:1414823713;T:1897501503;N:39037", 150, 150, null, null, 1941068575, 1341378672, 1414823713, 1897501503, 39037, "SRX13883467", "SRS11752236", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89423, 0.89602, 0.22595, 0.2243, 0.70212, 0.70112, 0.52954, 0.52253, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68392, "SRR17720619", "SRX13883466", "SRS11752235", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Hypoxia IP", "GSM5832277", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832277", "GSM5832277: m5C Hypoxia IP; Danio rerio; OTHER", "GSM5832277 r1", "GSM5832277", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Hypoxia_IP_R1.fastq.gz m5C_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 7837067100.0, 26123557.0, "GSM5832277 r1", "0:150 1:150", "A:1881167242;C:1973697370;G:2143523979;T:1838645554;N:32955", 150, 150, null, null, 1881167242, 1973697370, 2143523979, 1838645554, 32955, "SRX13883466", "SRS11752235", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87593, 0.87108, 0.45438, 0.45093, 0.71664, 0.7321, 0.67861, 0.69742, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68393, "SRR17720620", "SRX13883465", "SRS11752233", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Hypoxia Input", "GSM5832276", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832276", "GSM5832276: m5C Hypoxia Input; Danio rerio; OTHER", "GSM5832276 r1", "GSM5832276", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Hypoxia_Input_R1.fastq.gz m5C_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 8696183100.0, 28987277.0, "GSM5832276 r1", "0:150 1:150", "A:2564166903;C:1771446935;G:1858965930;T:2501551942;N:51390", 150, 150, null, null, 2564166903, 1771446935, 1858965930, 2501551942, 51390, "SRX13883465", "SRS11752233", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89379, 0.89585, 0.23898, 0.23828, 0.70272, 0.70278, 0.52965, 0.50047, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68394, "SRR17720621", "SRX13883464", "SRS11752234", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Normoxia IP", "GSM5832275", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832275", "GSM5832275: m1A Normoxia IP; Danio rerio; OTHER", "GSM5832275 r1", "GSM5832275", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Normoxia_IP_R1.fastq.gz m1A_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6882734400.0, 22942448.0, "GSM5832275 r1", "0:150 1:150", "A:1321946139;C:1977632664;G:2310916241;T:1272200359;N:38997", 150, 150, null, null, 1321946139, 1977632664, 2310916241, 1272200359, 38997, "SRX13883464", "SRS11752234", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.88367, 0.88951, 0.09774, 0.09525, 0.86395, 0.86401, 0.70125, 0.74894, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68395, "SRR17720622", "SRX13883463", "SRS11752232", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Normoxia Input", "GSM5832274", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832274", "GSM5832274: m1A Normoxia Input; Danio rerio; OTHER", "GSM5832274 r1", "GSM5832274", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Normoxia_Input_R1.fastq.gz m1A_Normoxia_Input_R2.fastq.gz", "fastq fastq", 7374452700.0, 24581509.0, "GSM5832274 r1", "0:150 1:150", "A:1511389847;C:2082118937;G:2325922232;T:1454979400;N:42284", 150, 150, null, null, 1511389847, 2082118937, 2325922232, 1454979400, 42284, "SRX13883463", "SRS11752232", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.94589, 0.94385, 0.18226, 0.18222, 0.80878, 0.8102, 0.73686, 0.71921, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68396, "SRR17720623", "SRX13883462", "SRS11752231", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Hypoxia IP", "GSM5832273", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832273", "GSM5832273: m1A Hypoxia IP; Danio rerio; OTHER", "GSM5832273 r1", "GSM5832273", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Hypoxia_IP_R1.fastq.gz m1A_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 4861573800.0, 16205246.0, "GSM5832273 r1", "0:150 1:150", "A:927063480;C:1355342107;G:1698345464;T:880801957;N:20792", 150, 150, null, null, 927063480, 1355342107, 1698345464, 880801957, 20792, "SRX13883462", "SRS11752231", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.8575, 0.86165, 0.10013, 0.09909, 0.87249, 0.87221, 0.72225, 0.66629, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68397, "SRR17720624", "SRX13883461", "SRS11752229", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Hypoxia Input", "GSM5832272", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832272", "GSM5832272: m1A Hypoxia Input; Danio rerio; OTHER", "GSM5832272 r1", "GSM5832272", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Hypoxia_Input_R1.fastq.gz m1A_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 7262130600.0, 24207102.0, "GSM5832272 r1", "0:150 1:150", "A:1553326396;C:2003023914;G:2214285414;T:1491453374;N:41502", 150, 150, null, null, 1553326396, 2003023914, 2214285414, 1491453374, 41502, "SRX13883461", "SRS11752229", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.94247, 0.94013, 0.20625, 0.20507, 0.80188, 0.80137, 0.70188, 0.73891, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 16, "expanded_columns": [], "expandable_columns": [], 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"run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], 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prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_selection\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "other", "p1": "bulk", "p2": "Nervous System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&technology=bulk&tissue_curation_coarse=Nervous+System", "results": [{"value": "OTHER", "label": "OTHER", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&technology=bulk&tissue_curation_coarse=Nervous+System&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, 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