run_metadata: 68394

This data as json

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
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.		pubmed:35135476		m1A Normoxia IP	GSM5832275		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’ 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® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		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® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP356476		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			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		China	2022-01-24	Adult	Adult	Brain	Nervous System