metadata: run_metadata: 6 rows where devstage_curation = "Segmentation" and tissue

6 rows where devstage_curation = "Segmentation" and tissue_curation = "Gonad"

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.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.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
43832	43832	SRR6163072	SRX3274594	SRS2585897	SRP119825	PRJNA414036	The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation	GSE104855	Transcriptome Analysis	Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis when extensive cell proliferation patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly they gain a gene expression profile reflecting differentiation into cells of different germ layers in a process that we could direct by expression of specific cell fate determinants. Importantly we visualized these events within live zebrafish embryos which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino	pubmed:29257950	13hpf PGC dead end MO 2	GSM2808858	tissue:germ cells\|agent:dead end MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	13hpf PGC dead end MO 2	post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin 2011 reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al. 2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al. 2012. Results not passing Cuffdiff’s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test was chosen. Data were subsequently divided into separate lists containing either up or downregulated transcripts. For gene ontology GO analysis a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al. 2013 and the “GO biological process complete” annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al. 2011 Reduce and visualize GO 0.9 similarity large and SimRel as a semantic similarity measure. Genome build: Zv9 Supplementary files format and content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions GO terms and REVIGO analysis for each up or downregulated group of genes	germ cells	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	agent:dead end MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	GSM2808858	GSM2808858: 13hpf PGC dead end MO 2; Danio rerio; RNA Seq	GSM2808858	1	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	GEO Accession:GSM2808858	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP119825	4_SIL443_04_S4_R1_001.fastq.gz 4_SIL443_04_S4_R2_001.fastq.gz	fastq fastq	8437981102.0	56604234.0	GSM2808858 r1	0:74.50 1:74.57	A:1860341053;C:1941389948;G:2080153476;T:2547414135;N:8682490	74	74	1860341053	1941389948	2080153476	2547414135	8682490	SRX3274594	SRS2585897	SRA619012	GEO	Erez Raz, Institute of Cell Biology, University Clinic Muenster	2	0.51323	0.44439	0.09069	0.07858	0.81278	0.8254	0.55336	0.55973	74	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2017-10-12	Segmentation	Embryo	Gonad	Reproductive System
43833	43833	SRR6163071	SRX3274593	SRS2585896	SRP119825	PRJNA414036	The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation	GSE104855	Transcriptome Analysis	Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis when extensive cell proliferation patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly they gain a gene expression profile reflecting differentiation into cells of different germ layers in a process that we could direct by expression of specific cell fate determinants. Importantly we visualized these events within live zebrafish embryos which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino	pubmed:29257950	13hpf PGC control MO 2	GSM2808857	tissue:germ cells\|agent:control MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	13hpf PGC control MO 2	post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin 2011 reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al. 2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al. 2012. Results not passing Cuffdiff’s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test was chosen. Data were subsequently divided into separate lists containing either up or downregulated transcripts. For gene ontology GO analysis a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al. 2013 and the “GO biological process complete” annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al. 2011 Reduce and visualize GO 0.9 similarity large and SimRel as a semantic similarity measure. Genome build: Zv9 Supplementary files format and content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions GO terms and REVIGO analysis for each up or downregulated group of genes	germ cells	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	agent:control MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	GSM2808857	GSM2808857: 13hpf PGC control MO 2; Danio rerio; RNA Seq	GSM2808857	1	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	GEO Accession:GSM2808857	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP119825	3_SIL443_03_S3_R1_001.fastq.gz 3_SIL443_03_S3_R2_001.fastq.gz	fastq fastq	14659988852.0	98369149.0	GSM2808857 r1	0:74.46 1:74.57	A:3084007102;C:3643125037;G:3850785284;T:4067653493;N:14417936	74	74	3084007102	3643125037	3850785284	4067653493	14417936	SRX3274593	SRS2585896	SRA619012	GEO	Erez Raz, Institute of Cell Biology, University Clinic Muenster	2	0.52834	0.48226	0.12373	0.11352	0.80107	0.81351	0.60825	0.63394	74	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2017-10-12	Segmentation	Embryo	Gonad	Reproductive System
43834	43834	SRR6163070	SRX3274592	SRS2585895	SRP119825	PRJNA414036	The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation	GSE104855	Transcriptome Analysis	Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis when extensive cell proliferation patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly they gain a gene expression profile reflecting differentiation into cells of different germ layers in a process that we could direct by expression of specific cell fate determinants. Importantly we visualized these events within live zebrafish embryos which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino	pubmed:29257950	13hpf PGC dead end MO 1	GSM2808856	tissue:germ cells\|agent:dead end MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	13hpf PGC dead end MO 1	post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin 2011 reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al. 2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al. 2012. Results not passing Cuffdiff’s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test was chosen. Data were subsequently divided into separate lists containing either up or downregulated transcripts. For gene ontology GO analysis a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al. 2013 and the “GO biological process complete” annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al. 2011 Reduce and visualize GO 0.9 similarity large and SimRel as a semantic similarity measure. Genome build: Zv9 Supplementary files format and content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions GO terms and REVIGO analysis for each up or downregulated group of genes	germ cells	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	agent:dead end MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	GSM2808856	GSM2808856: 13hpf PGC dead end MO 1; Danio rerio; RNA Seq	GSM2808856	1	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	GEO Accession:GSM2808856	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP119825	2_SIL443_02_S2_R2_001.fastq.gz 2_SIL443_02_S2_R1_001.fastq.gz	fastq fastq	6698714120.0	44941592.0	GSM2808856 r1	0:74.48 1:74.57	A:1382110759;C:1666182128;G:1762655710;T:1881061600;N:6703923	74	74	1382110759	1666182128	1762655710	1881061600	6703923	SRX3274592	SRS2585895	SRA619012	GEO	Erez Raz, Institute of Cell Biology, University Clinic Muenster	2	0.58574	0.53597	0.15277	0.13856	0.8226	0.83169	0.64247	0.44471	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2017-10-12	Segmentation	Embryo	Gonad	Reproductive System
43835	43835	SRR6163069	SRX3274591	SRS2585894	SRP119825	PRJNA414036	The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation	GSE104855	Transcriptome Analysis	Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis when extensive cell proliferation patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly they gain a gene expression profile reflecting differentiation into cells of different germ layers in a process that we could direct by expression of specific cell fate determinants. Importantly we visualized these events within live zebrafish embryos which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino	pubmed:29257950	13hpf PGC control MO 1	GSM2808855	tissue:germ cells\|agent:control MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	13hpf PGC control MO 1	post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin 2011 reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al. 2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al. 2012. Results not passing Cuffdiff’s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test was chosen. Data were subsequently divided into separate lists containing either up or downregulated transcripts. For gene ontology GO analysis a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al. 2013 and the “GO biological process complete” annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al. 2011 Reduce and visualize GO 0.9 similarity large and SimRel as a semantic similarity measure. Genome build: Zv9 Supplementary files format and content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions GO terms and REVIGO analysis for each up or downregulated group of genes	germ cells	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	agent:control MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	GSM2808855	GSM2808855: 13hpf PGC control MO 1; Danio rerio; RNA Seq	GSM2808855	1	PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific	GEO Accession:GSM2808855	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP119825	1_SIL443_01_S1_R1_001.fastq.gz 1_SIL443_01_S1_R2_001.fastq.gz	fastq fastq	5496482855.0	36876415.0	GSM2808855 r1	0:74.48 1:74.57	A:1211902681;C:1356435115;G:1443569780;T:1478848150;N:5727129	74	74	1211902681	1356435115	1443569780	1478848150	5727129	SRX3274591	SRS2585894	SRA619012	GEO	Erez Raz, Institute of Cell Biology, University Clinic Muenster	2	0.66316	0.5871	0.16838	0.14743	0.7824	0.79511	0.63777	0.50198	74	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2017-10-12	Segmentation	Embryo	Gonad	Reproductive System
60889	60889	SRR12628232	SRX9110495	SRS7353478	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h11 2: PGCs 11hpf repeat2	GSM4777192	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h11 2: PGCs 11hpf repeat2	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777192	GSM4777192: h11 2: PGCs 11hpf repeat2; Danio rerio; miRNA Seq	GSM4777192	1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777192	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h11_2.fastq	fastq	1725506100.0	11503374.0	GSM4777192 r1	0:150 1:0	A:419294958;C:415643261;G:432730446;T:457808038;N:29397	150	0	419294958	415643261	432730446	457808038	29397	SRX9110495	SRS7353478	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00062		0.0		0.99991		1.0		150		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Segmentation	Embryo	Gonad	Reproductive System
60890	60890	SRR12628231	SRX9110494	SRS7353477	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h11 1: PGCs 11hpf repeat1	GSM4777191	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h11 1: PGCs 11hpf repeat1	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777191	GSM4777191: h11 1: PGCs 11hpf repeat1; Danio rerio; miRNA Seq	GSM4777191	1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777191	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h11_1.fastq	fastq	2690366550.0	17935777.0	GSM4777191 r1	0:150 1:0	A:722881530;C:687611993;G:633563837;T:646263376;N:45814	150	0	722881530	687611993	633563837	646263376	45814	SRX9110494	SRS7353477	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.0006		0.0		0.99991		1.0		150		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Segmentation	Embryo	Gonad	Reproductive System

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