metadata: run_metadata: 8 rows where devstage_curation = "Blastula" and experiment.library

8 rows where devstage_curation = "Blastula" and experiment.library_strategy = "miRNA-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
41430	41430	SRR4423106	SRX2245290	SRS1745854	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development			Time course 3 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:zfs:0000015 stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal							miRNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf	348 3	348 3	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S03small.fastq	fastq	1025732824.0	7452991.0	S03small.fastq	0:137.63	A:225573059;C:298586545;G:288470386;T:213102834;N:0	137		225573059	298586545	288470386	213102834	0	SRX2245290	SRS1745854	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.8983	0.04271	0.95546	0.91281	159	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41433	41433	SRR4423103	SRX2245287	SRS1745852	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development			Time course 2 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:high stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal							miRNA Seq of Zebrafish: high stage3.3 hpf	348 2	348 2	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S02small.fastq	fastq	304535574.0	3376105.0	S02small.fastq	0:90.20	A:69193719;C:84372087;G:86707481;T:64262287;N:0	90		69193719	84372087	86707481	64262287	0	SRX2245287	SRS1745852	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.56812	0.09695	0.93474	0.93654	51	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57186	57186	SRR11263444	SRX7870077	SRS6278494	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061	miRNA of MZdgcr8 3	GSM4396432	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	miRNA of MZdgcr8 3	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	GSM4396432	GSM4396432: miRNA of MZdgcr8 3; Danio rerio; miRNA Seq	GSM4396432		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396432	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	MZ_3_miRNA.fq.gz	fastq	602855750.0	12057115.0	GSM4396432 r1	0:50 1:0	A:146678206;C:139956283;G:181049484;T:135139840;N:31937	50	0	146678206	139956283	181049484	135139840	31937	SRX7870077	SRS6278494	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.00091	0.0001	0.9987	0.73076	50	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57187	57187	SRR11263443	SRX7870076	SRS6278493	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061	miRNA of MZdgcr8 2	GSM4396431	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	miRNA of MZdgcr8 2	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	GSM4396431	GSM4396431: miRNA of MZdgcr8 2; Danio rerio; miRNA Seq	GSM4396431		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396431	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	MZ_2_miRNA.fq.gz	fastq	532605954.0	10443254.0	GSM4396431 r1	0:51 1:0	A:124901241;C:134604417;G:148078897;T:124932015;N:89384	51	0	124901241	134604417	148078897	124932015	89384	SRX7870076	SRS6278493	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.0002	2e-05	0.99935	0.51428	51	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57188	57188	SRR11263442	SRX7870075	SRS6278492	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061	miRNA of MZdgcr8 1	GSM4396430	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	miRNA of MZdgcr8 1	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	GSM4396430	GSM4396430: miRNA of MZdgcr8 1; Danio rerio; miRNA Seq	GSM4396430		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396430	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	MZ_1_miRNA.fq.gz	fastq	588374148.0	11536748.0	GSM4396430 r1	0:51 1:0	A:137533072;C:149724383;G:163915952;T:137198731;N:2010	51	0	137533072	149724383	163915952	137198731	2010	SRX7870075	SRS6278492	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.0014	0.00031	0.99795	0.62441	51	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57189	57189	SRR11263441	SRX7870074	SRS6278490	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061	miRNA of Wild type 3	GSM4396429	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	miRNA of Wild type 3	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	GSM4396429	GSM4396429: miRNA of Wild type 3; Danio rerio; miRNA Seq	GSM4396429		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396429	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	WT_3_miRNA.fq.gz	fastq	688929450.0	13778589.0	GSM4396429 r1	0:50 1:0	A:171239999;C:140558088;G:209452609;T:167641448;N:37306	50	0	171239999	140558088	209452609	167641448	37306	SRX7870074	SRS6278490	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.00247	0.00016	0.99797	0.60356	50	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57190	57190	SRR11263440	SRX7870073	SRS6278491	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061	miRNA of Wild type 2	GSM4396428	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	miRNA of Wild type 2	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	GSM4396428	GSM4396428: miRNA of Wild type 2; Danio rerio; miRNA Seq	GSM4396428		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396428	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	WT_2_miRNA.fq.gz	fastq	680017935.0	13333685.0	GSM4396428 r1	0:51 1:0	A:161673690;C:168811670;G:190321246;T:159208682;N:2647	51	0	161673690	168811670	190321246	159208682	2647	SRX7870073	SRS6278491	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.03809	0.00119	0.99318	0.59584	51	B	usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57191	57191	SRR11263439	SRX7870072	SRS6278489	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061	miRNA of Wild type 1	GSM4396427	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	miRNA of Wild type 1	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	GSM4396427	GSM4396427: miRNA of Wild type 1; Danio rerio; miRNA Seq	GSM4396427		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396427	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	WT_1_miRNA.fq.gz	fastq	606884853.0	11899703.0	GSM4396427 r1	0:51 1:0	A:144656910;C:150045615;G:169161904;T:143018153;N:2271	51	0	144656910	150045615	169161904	143018153	2271	SRX7870072	SRS6278489	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.0559	0.00242	0.99064	0.54228	51	B	usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	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");;