metadata: run_metadata: 19 rows where devstage_curation = "Pharyngula" and experiment.library

19 rows where devstage_curation = "Pharyngula" and experiment.library_strategy = "RIP-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
41511	41511	SRR5004963	SRX2336797	SRS1790193	SRP092907	PRJNA352850	Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos	GSE89655	Other	RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells	pubmed:28869969	zebrafish embryos ythdf2 RIP rep2	GSM2386192	source name:zebrafish embryos\|genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	zebrafish embryos ythdf2 RIP rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software	zebrafish embryos		For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.		genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	GSM2386192	GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq	GSM2386192		1	For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.	GEO Accession:GSM2386192	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP092907		ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz	fastq fastq	4007024510.0	19836755.0	GSM2386192 r1	0:101 1:101	A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309	101	101	769487104	1245093129	1251328145	740377823	738309	SRX2336797	SRS1790193	SRA491654	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.97768	0.97802	0.22786	0.21743	0.89885	0.89968	0.77584	0.83808	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	bulk	bulk	China	2016-11-08	Pharyngula	Embryo	Trunk	Surface Structure
41512	41512	SRR5004962	SRX2336796	SRS1790194	SRP092907	PRJNA352850	Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos	GSE89655	Other	RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells	pubmed:28869969	zebrafish embryos ythdf2 RIP rep1	GSM2386191	source name:zebrafish embryos\|genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	zebrafish embryos ythdf2 RIP rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software	zebrafish embryos		For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.		genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	GSM2386191	GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq	GSM2386191		1	For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.	GEO Accession:GSM2386191	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP092907		ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz	fastq fastq	6144583662.0	30418731.0	GSM2386191 r1	0:101 1:101	A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305	101	101	1227614258	1869131844	1825793436	1220118819	1925305	SRX2336796	SRS1790194	SRA491654	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.96857	0.96917	0.23397	0.22377	0.89832	0.90147	0.78619	0.8258	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	bulk	bulk	China	2016-11-08	Pharyngula	Embryo	Trunk	Surface Structure
42000	42000	SRR5379364	SRX2674572	SRS2073700	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.	pubmed:29636379	ddx39a 24hpf RIPseq	GSM2550918	source name:embryos\|genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	ddx39a 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	GSM2550918	GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550918		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550918	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513		RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz	fastq fastq	3819239400.0	19096197.0	GSM2550918 r1	0:100 1:100	A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472	100	100	751858949	1169790479	1139713624	756987876	888472	SRX2674572	SRS2073700	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.98659	0.98572	0.28836	0.28975	0.89422	0.89558	0.75396	0.78553	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
42001	42001	SRR5379363	SRX2674571	SRS2073697	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.	pubmed:29636379	WT 24hpf RIPseq	GSM2550917	source name:embryos\|genotype:wild type\|tissue:embryo\|developmental stage:24hpf	WT 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:wild type\|tissue:embryo\|developmental stage:24hpf	GSM2550917	GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550917		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550917	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513		RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz	fastq fastq	3802882200.0	19014411.0	GSM2550917 r1	0:100 1:100	A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137	100	100	733911232	1178365174	1154031422	735690235	884137	SRX2674571	SRS2073697	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.9866	0.98469	0.30567	0.30486	0.90796	0.90928	0.82926	0.83029	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
53427	53427	SRR9854014	SRX6608456	SRS5172704	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants		RBM8A RIPSEQ Rep3	GSM3983830	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep3	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983830	GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq	GSM3983830		1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983830	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB3.fastq.gz	fastq	1174462616.0	32753220.0	GSM3983830 r1	0:35.86	A:277856243;C:303697175;G:340240303;T:252574884;N:94011	35		277856243	303697175	340240303	252574884	94011	SRX6608456	SRS5172704	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.90426		0.1746		0.77341		0.57553		35		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
53428	53428	SRR9854013	SRX6608455	SRS5172702	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants		RBM8A RIPSEQ Rep2	GSM3983829	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep2	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983829	GSM3983829: RBM8A RIPSEQ Rep2; Danio rerio; RIP Seq	GSM3983829		1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983829	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB2.fastq.gz	fastq	65641776.0	2466295.0	GSM3983829 r1	0:26.62	A:18933213;C:16060113;G:13492679;T:17151951;N:3820	26		18933213	16060113	13492679	17151951	3820	SRX6608455	SRS5172702	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.17621		0.02351		0.88069		0.60622		15		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
53429	53429	SRR9854012	SRX6608454	SRS5172701	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants		RBM8A RIPSEQ Rep1	GSM3983828	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep1	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983828	GSM3983828: RBM8A RIPSEQ Rep1; Danio rerio; RIP Seq	GSM3983828		1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983828	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB1.fastq.gz	fastq	403183413.0	11908151.0	GSM3983828 r1	0:33.86	A:80085450;C:111343041;G:140916198;T:70619085;N:219639	33		80085450	111343041	140916198	70619085	219639	SRX6608454	SRS5172701	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.862		0.1026		0.95359		0.79372		33		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
71624	71624	SRR21849078	SRX17837652	SRS15359804	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.		33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 2	Zebrafish 33 hpf.Bulk RIP seq.Flag hCsde1 2	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:8\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 2	Flag hCsde1 2	Flag hCsde1 2	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Flag-hCsde1-2_1.fq.gz Flag-hCsde1-2_2.fq.gz	fastq fastq	7253178600.0	24177262.0	Flag hCsde1 2 1.fq.gz	0:150 1:150	A:1490001899;C:2113749179;G:2152941566;T:1496406491;N:79465	150	150	1490001899	2113749179	2152941566	1496406491	79465	SRX17837652	SRS15359804	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.9907	0.98973	0.51575	0.5119	0.9459	0.94631	0.80609	0.80353	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
71625	71625	SRR21849079	SRX17837651	SRS15359803	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.		33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 1	Zebrafish 33 hpf.Bulk RIP seq.Flag hCsde1 1	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:7\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 1	Flag hCsde1 1	Flag hCsde1 1	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Flag-hCsde1-1_1.fq.gz Flag-hCsde1-1_2.fq.gz	fastq fastq	5032252500.0	16774175.0	Flag hCsde1 1 1.fq.gz	0:150 1:150	A:1150344713;C:1135461821;G:1687878347;T:1058543429;N:24190	150	150	1150344713	1135461821	1687878347	1058543429	24190	SRX17837651	SRS15359803	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.22813	0.23161	0.06226	0.06317	0.92801	0.92719	0.73744	0.71685	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
71626	71626	SRR21849080	SRX17837650	SRS15359801	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.		33 hpf Zebrafish Bulk RIP seq.Control2	Zebrafish 33 hpf.Bulk RIP seq.Control2	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:6\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Control2	Control2	Control2	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Control2_1.fq.gz Control2_2.fq.gz	fastq fastq	7884108600.0	26280362.0	Control2 1.fq.gz	0:150 1:150	A:1586894082;C:2334065454;G:2372509011;T:1590552802;N:87251	150	150	1586894082	2334065454	2372509011	1590552802	87251	SRX17837650	SRS15359801	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.98745	0.98691	0.48401	0.48011	0.94095	0.94113	0.74796	0.74138	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
71627	71627	SRR21849081	SRX17837649	SRS15359800	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.		33 hpf Zebrafish Bulk RIP seq.Control1	Zebrafish 33 hpf.Bulk RIP seq.Control1	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:5\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Control1	Control1	Control1	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Control1_1.fq.gz Control1_2.fq.gz	fastq fastq	6838591200.0	22795304.0	Control1 1.fq.gz	0:150 1:150	A:1483754703;C:1578056923;G:2412990846;T:1363739708;N:49020	150	150	1483754703	1578056923	2412990846	1363739708	49020	SRX17837649	SRS15359800	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.34381	0.34082	0.09181	0.09135	0.95144	0.95148	0.81928	0.81462	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
72384	72384	SRR22805230	SRX18764963	SRS16199859	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		28	28.ythdf2 MO m6A meRIP replicate 2	strain:AB\|isolate:28\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									28.ythdf2 MO m6A meRIP replicate 2	28	28	28			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		ythdf2_MO_m6A_meRIP_replicate_2_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	7361721649.0	26446542.0	ythdf2 MO m6A meRIP replicate 2 R1.fastq.gz	0:139.19 1:139.17	A:1963471349;C:1716978769;G:1713549467;T:1967688429;N:33635	139	139	1963471349	1716978769	1713549467	1967688429	33635	SRX18764963	SRS16199859	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95246	0.9547	0.1386	0.13796	0.69757	0.69593	0.44772	0.44911	138	138	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72385	72385	SRR22805231	SRX18764962	SRS16199858	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		27	27.ythdf2 MO m6A meRIP replicate 1	strain:AB\|isolate:27\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									27.ythdf2 MO m6A meRIP replicate 1	27	27	27			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		ythdf2_MO_m6A_meRIP_replicate_1_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7064658336.0	25169165.0	ythdf2 MO m6A meRIP replicate 1 R1.fastq.gz	0:140.35 1:140.33	A:1889792523;C:1642179006;G:1639348147;T:1893307582;N:31078	140	140	1889792523	1642179006	1639348147	1893307582	31078	SRX18764962	SRS16199858	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95312	0.95495	0.14782	0.14808	0.69856	0.69656	0.46053	0.45683	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72386	72386	SRR22805232	SRX18764961	SRS16199857	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		26	26.Control knockdown m6A meRIP replicate 2	strain:AB\|isolate:26\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									26.Control knockdown m6A meRIP replicate 2	26	26	26			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		Control_knockdown_m6A_meRIP_replicate_2_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	6960835520.0	25210812.0	Control knockdown m6A meRIP replicate 2 R1.fastq.gz	0:138.06 1:138.04	A:1851748550;C:1628253635;G:1624430306;T:1856371475;N:31554	138	138	1851748550	1628253635	1624430306	1856371475	31554	SRX18764961	SRS16199857	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95077	0.95337	0.12974	0.13019	0.69846	0.69737	0.45561	0.45724	134	134	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72387	72387	SRR22805233	SRX18764960	SRS16199856	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		25	25.Control knockdown m6A meRIP replicate 1	strain:AB\|isolate:25\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									25.Control knockdown m6A meRIP replicate 1	25	25	25			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		Control_knockdown_m6A_meRIP_replicate_1_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7116588450.0	25626978.0	Control knockdown m6A meRIP replicate 1 R1.fastq.gz	0:138.86 1:138.84	A:1872021500;C:1685125220;G:1683152373;T:1876257768;N:31589	138	138	1872021500	1685125220	1683152373	1876257768	31589	SRX18764960	SRS16199856	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95363	0.95468	0.05483	0.05373	0.76777	0.76648	0.4523	0.45215	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72393	72393	SRR22805239	SRX18764954	SRS16199850	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		20	20.BHbisPhenolF 10uM m6A meRIP replicate 2	strain:AB\|isolate:20\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									20.BHbisPhenolF 10uM m6A meRIP replicate 2	20	20	20			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		BHPF_10uM_m6A_meRIP_replicate_2_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	7491317369.0	26658666.0	BHbisPhenolF 10uM m6A meRIP replicate 2 R1.fastq.gz	0:140.51 1:140.49	A:1978702731;C:1766538897;G:1763052208;T:1982989954;N:33579	140	140	1978702731	1766538897	1763052208	1982989954	33579	SRX18764954	SRS16199850	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.9529	0.95443	0.08298	0.08205	0.68891	0.68846	0.47278	0.47013	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72394	72394	SRR22805240	SRX18764953	SRS16199849	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		19	19.BHbisPhenolF 10uM m6A meRIP replicate 1	strain:AB\|isolate:19\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									19.BHbisPhenolF 10uM m6A meRIP replicate 1	19	19	19			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		BHPF_10uM_m6A_meRIP_replicate_1_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7103220388.0	25558854.0	BHbisPhenolF 10uM m6A meRIP replicate 1 R1.fastq.gz	0:138.97 1:138.95	A:1882505135;C:1667796740;G:1665421739;T:1887465071;N:31703	138	138	1882505135	1667796740	1665421739	1887465071	31703	SRX18764953	SRS16199849	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95261	0.95474	0.09233	0.09094	0.69794	0.6966	0.46269	0.46455	111	111	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72395	72395	SRR22805241	SRX18764952	SRS16199848	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		18	18.DMSO control m6A meRIP replicate 2	strain:AB\|isolate:18\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									18.DMSO control m6A meRIP replicate 2	18	18	18			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		DMSO_control_m6A_meRIP_replicate_2_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	7608584716.0	27081562.0	DMSO control m6A meRIP replicate 2 R1.fastq.gz	0:140.48 1:140.47	A:2016159583;C:1788089257;G:1783486901;T:2020815087;N:33888	140	140	2016159583	1788089257	1783486901	2020815087	33888	SRX18764952	SRS16199848	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.9526	0.95462	0.08497	0.08367	0.69822	0.69755	0.46646	0.4688	114	114	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72396	72396	SRR22805242	SRX18764951	SRS16199847	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity		17	17.DMSO control m6A meRIP replicate 1	strain:AB\|isolate:17\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									17.DMSO control m6A meRIP replicate 1	17	17	17			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		DMSO_control_m6A_meRIP_replicate_1_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7394836277.0	26199072.0	DMSO control m6A meRIP replicate 1 R1.fastq.gz	0:141.14 1:141.12	A:1964011730;C:1732461692;G:1728237059;T:1970092128;N:33668	141	141	1964011730	1732461692	1728237059	1970092128	33668	SRX18764951	SRS16199847	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95315	0.95536	0.1083	0.1071	0.70694	0.70587	0.47144	0.47082	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;