metadata: run_metadata: 9 rows where devstage_curation = "Gastrula" and experiment.library

9 rows where devstage_curation = "Gastrula" and experiment.library_selection = "PCR"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	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
48732	48732	SRR7789586	SRX4644417	SRS3742487	SRP159670	PRJNA475635	Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis	PRJNA475635	Other	The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.			TDCIPP 6hpf 5 S15	strain:5D\|isolate:102\|dev stage:6 hpf\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal	TDCIPP 6hpf 5 S15	TDCIPP 6hpf 5 S15	TDCIPP 6hpf 5 S15	Nextera XT DNA Library Prep kit	AMPLICON	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina MiniSeq	SRP159670	TDCIPP-6hpf-5_S15_L001_R1_001.fastq.gz TDCIPP-6hpf-5_S15_L001_R2_001.fastq.gz	fastq fastq	103436592.0	515633.0	TDCIPP 6hpf 5 S15 L001 R2 001.fastq.gz	0:100.23 1:100.37	A:26213221;C:25393681;G:25395332;T:25877353;N:557005	100	100	26213221	25393681	25395332	25877353	557005	SRX4644417	SRS3742487	SRA767209	University of California, Riverside\|Environmental Sciences	University of California, Riverside	2	0.9545	0.9544	0.00043	0.0004	0.99898	0.99904	0.33908	0.3596	64	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	nextera	bulk	unknown	unknown	United States	2018-09-05	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48733	48733	SRR7789587	SRX4644416	SRS3742486	SRP159670	PRJNA475635	Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis	PRJNA475635	Other	The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.			TDCIPP 6hpf 3 S14	strain:5D\|isolate:101\|dev stage:6 hpf\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal	TDCIPP 6hpf 3 S14	TDCIPP 6hpf 3 S14	TDCIPP 6hpf 3 S14	Nextera XT DNA Library Prep kit	AMPLICON	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina MiniSeq	SRP159670	TDCIPP-6hpf-3_S14_L001_R1_001.fastq.gz TDCIPP-6hpf-3_S14_L001_R2_001.fastq.gz	fastq fastq	99767681.0	500238.0	TDCIPP 6hpf 3 S14 L001 R2 001.fastq.gz	0:99.64 1:99.80	A:25255312;C:24464400;G:24481390;T:25002218;N:564361	99	99	25255312	24464400	24481390	25002218	564361	SRX4644416	SRS3742486	SRA767209	University of California, Riverside\|Environmental Sciences	University of California, Riverside	2	0.96117	0.96052	0.00028	0.00028	0.99924	0.99922	0.35418	0.35375	148	149	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	nextera	bulk	unknown	unknown	United States	2018-09-05	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48752	48752	SRR7789606	SRX4644397	SRS3742467	SRP159670	PRJNA475635	Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis	PRJNA475635	Other	The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.			DMSO 6hpf 5 S6	strain:5D\|isolate:99\|dev stage:6 hpf\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal	DMSO 6hpf 5 S6	DMSO 6hpf 5 S6	DMSO 6hpf 5 S6	Nextera XT DNA Library Prep kit	AMPLICON	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina MiniSeq	SRP159670	DMSO-6hpf-5_S6_L001_R1_001.fastq.gz DMSO-6hpf-5_S6_L001_R2_001.fastq.gz	fastq fastq	107736291.0	525615.0	DMSO 6hpf 5 S6 L001 R2 001.fastq.gz	0:102.38 1:102.59	A:27251903;C:26520518;G:26567935;T:26878661;N:517274	102	102	27251903	26520518	26567935	26878661	517274	SRX4644397	SRS3742467	SRA767209	University of California, Riverside\|Environmental Sciences	University of California, Riverside	2	0.96019	0.95982	0.00045	0.00043	0.99918	0.99916	0.37174	0.3343	151	148	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	nextera	bulk	unknown	unknown	United States	2018-09-05	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48753	48753	SRR7789607	SRX4644396	SRS3742466	SRP159670	PRJNA475635	Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis	PRJNA475635	Other	The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.			TDCIPP 6hpf 1 S13	strain:5D\|isolate:100\|dev stage:6 hpf\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal	TDCIPP 6hpf 1 S13	TDCIPP 6hpf 1 S13	TDCIPP 6hpf 1 S13	Nextera XT DNA Library Prep kit	AMPLICON	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina MiniSeq	SRP159670	TDCIPP-6hpf-1_S13_L001_R2_001.fastq.gz TDCIPP-6hpf-1_S13_L001_R1_001.fastq.gz	fastq fastq	91271391.0	448917.0	TDCIPP 6hpf 1 S13 L001 R2 001.fastq.gz	0:101.61 1:101.71	A:23269221;C:22266290;G:22291849;T:22983659;N:460372	101	101	23269221	22266290	22291849	22983659	460372	SRX4644396	SRS3742466	SRA767209	University of California, Riverside\|Environmental Sciences	University of California, Riverside	2	0.96069	0.96135	0.0005	0.00051	0.99916	0.99916	0.34621	0.3774	76	76	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	nextera	bulk	unknown	unknown	United States	2018-09-05	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48760	48760	SRR7789614	SRX4644389	SRS3742459	SRP159670	PRJNA475635	Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis	PRJNA475635	Other	The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.			DMSO 6hpf 1 S4	strain:5D\|isolate:97\|dev stage:6 hpf\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal	DMSO 6hpf 1 S4	DMSO 6hpf 1 S4	DMSO 6hpf 1 S4	Nextera XT DNA Library Prep kit	AMPLICON	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina MiniSeq	SRP159670	DMSO-6hpf-1_S4_L001_R2_001.fastq.gz DMSO-6hpf-1_S4_L001_R1_001.fastq.gz	fastq fastq	95806388.0	464892.0	DMSO 6hpf 1 S4 L001 R2 001.fastq.gz	0:103.02 1:103.07	A:24562000;C:23294432;G:23307788;T:24218011;N:424157	103	103	24562000	23294432	23307788	24218011	424157	SRX4644389	SRS3742459	SRA767209	University of California, Riverside\|Environmental Sciences	University of California, Riverside	2	0.95656	0.95712	0.0004	0.00039	0.99918	0.99916	0.34071	0.34145	94	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	nextera	bulk	unknown	unknown	United States	2018-09-05	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
48761	48761	SRR7789615	SRX4644388	SRS3742458	SRP159670	PRJNA475635	Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis	PRJNA475635	Other	The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.			DMSO 6hpf 3 S5	strain:5D\|isolate:98\|dev stage:6 hpf\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal	DMSO 6hpf 3 S5	DMSO 6hpf 3 S5	DMSO 6hpf 3 S5	Nextera XT DNA Library Prep kit	AMPLICON	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina MiniSeq	SRP159670	DMSO-6hpf-3_S5_L001_R1_001.fastq.gz DMSO-6hpf-3_S5_L001_R2_001.fastq.gz	fastq fastq	105210098.0	508250.0	DMSO 6hpf 3 S5 L001 R1 001.fastq.gz	0:103.44 1:103.57	A:26828273;C:25677269;G:25721655;T:26524232;N:458669	103	103	26828273	25677269	25721655	26524232	458669	SRX4644388	SRS3742458	SRA767209	University of California, Riverside\|Environmental Sciences	University of California, Riverside	2	0.95583	0.95513	0.00047	0.00045	0.99916	0.99918	0.30844	0.29023	42	42	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	nextera	bulk	unknown	unknown	United States	2018-09-05	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
52147	52147	SRR8953735	SRX5733574	SRS4646934	SRP193814	PRJNA535392	Transcriptome analysis and identification of insecticide metabolism related genes post exposure to insecticide in Sitobion avenae	PRJNA535392	Other	Aphids causes serious lost in the production of wheat. Grain aphid Sitobion avenae is the dominant species of aphid in all wheat region of China and this species is also considered resistant to a variety of insecticides including imidacloprid and chlorpyrifos. However the resistance and metabolize mechanism of insecticides for S. avenae is still unclear. This study employed transcriptome analysis to compare the expression patterns of stress response genes under imidacloprid and chlorpyrifos for 15min 3h and 36h'exposure. post compared insecticide treated samples of different time duration to control sample we obtained 60 to 2267 Differential Express Unigenes DEUs among these DEUs 31 790 unigenes was classified into 66 786 categories of GO function group and 24 to 760 DEUs could be mapped into 54 to 268 KEGG pathways. The expression of DEUs related to insecticide metabolism related genes were analyzed. In the insecticide metabolism related genes cuticle protein is the largest group in DEUs and the second largest is ABC transporter. Our study will facilitate molecular research on insecticide resistance in S. avenae as well as in other wheat aphids.	20 miR 430 / embryos at shield stage were collected for RNA seq analsysis	MiR 430 /	M6	strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:Hong Kong\|age:6 hpf stage:shield stage\|sex:pooled male and female\|tissue:embyos\|phenotype:MiR 430 / \|sample type:embryos\|treatment:miR 430 was deleted by TALENs\|BioSampleModel:Model organism or animal	Transcriptome analysis and identification of insecticidemetabolism related genes post exposure to insecticide in Sitobion avenae	CH36h 3	CH36h 3	CH36h 3	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP193814	CH36h_3_S108_L004_R1_001.fastq.gz CH36h_3_S108_L004_R2_001.fastq.gz	fastq fastq	7952910884.0	26334142.0	CH36h 3 S108 L004 R1 001.fastq.gz	0:151 1:151	A:2299365607;C:1663413532;G:1659057469;T:2331018176;N:56100	151	151	2299365607	1663413532	1659057469	2331018176	56100	SRX5733574	SRS4646934	SRA879464	Institute of Plant Protection and Agro-Products Safety\|Anhui Academy of Agricultural Sciences	Institute of Plant Protection and Agro-Products Safety	2	7e-05	6e-05	1e-05	2e-05	0.99987	0.99989	0.44444	0.66666	151	151	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-24	Gastrula	Embryo	Whole Organism	All anatomical structures
52148	52148	SRR8953736	SRX5733573	SRS4646933	SRP193814	PRJNA535392	Transcriptome analysis and identification of insecticide metabolism related genes post exposure to insecticide in Sitobion avenae	PRJNA535392	Other	Aphids causes serious lost in the production of wheat. Grain aphid Sitobion avenae is the dominant species of aphid in all wheat region of China and this species is also considered resistant to a variety of insecticides including imidacloprid and chlorpyrifos. However the resistance and metabolize mechanism of insecticides for S. avenae is still unclear. This study employed transcriptome analysis to compare the expression patterns of stress response genes under imidacloprid and chlorpyrifos for 15min 3h and 36h'exposure. post compared insecticide treated samples of different time duration to control sample we obtained 60 to 2267 Differential Express Unigenes DEUs among these DEUs 31 790 unigenes was classified into 66 786 categories of GO function group and 24 to 760 DEUs could be mapped into 54 to 268 KEGG pathways. The expression of DEUs related to insecticide metabolism related genes were analyzed. In the insecticide metabolism related genes cuticle protein is the largest group in DEUs and the second largest is ABC transporter. Our study will facilitate molecular research on insecticide resistance in S. avenae as well as in other wheat aphids.	20 WT embryos at shield stage were collected for RNA seq analsysis	WT	W6	strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:Hong Kong\|age:6 hpf stage:shield stage\|sex:pooled male and female\|tissue:embyos\|phenotype:WT\|sample type:embryos\|treatment:Control\|BioSampleModel:Model organism or animal	Transcriptome analysis and identification of insecticidemetabolism related genes post exposure to insecticide in Sitobion avenae	CH36h 2	CH36h 2	CH36h 2	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP193814	CH36h_2_S107_L004_R1_001.fastq.gz CH36h_2_S107_L004_R2_001.fastq.gz	fastq fastq	7678237958.0	25424629.0	CH36h 2 S107 L004 R1 001.fastq.gz	0:151 1:151	A:2234219717;C:1589496206;G:1588910161;T:2265558614;N:53260	151	151	2234219717	1589496206	1588910161	2265558614	53260	SRX5733573	SRS4646933	SRA879464	Institute of Plant Protection and Agro-Products Safety\|Anhui Academy of Agricultural Sciences	Institute of Plant Protection and Agro-Products Safety	2	3e-05	2e-05	0.0	0.0	0.99993	0.99995	0.5	1.0	151	151	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-24	Gastrula	Embryo	Whole Organism	All anatomical structures
52149	52149	SRR8953738	SRX5733571	SRS4646935	SRP193814	PRJNA535392	Transcriptome analysis and identification of insecticide metabolism related genes post exposure to insecticide in Sitobion avenae	PRJNA535392	Other	Aphids causes serious lost in the production of wheat. Grain aphid Sitobion avenae is the dominant species of aphid in all wheat region of China and this species is also considered resistant to a variety of insecticides including imidacloprid and chlorpyrifos. However the resistance and metabolize mechanism of insecticides for S. avenae is still unclear. This study employed transcriptome analysis to compare the expression patterns of stress response genes under imidacloprid and chlorpyrifos for 15min 3h and 36h'exposure. post compared insecticide treated samples of different time duration to control sample we obtained 60 to 2267 Differential Express Unigenes DEUs among these DEUs 31 790 unigenes was classified into 66 786 categories of GO function group and 24 to 760 DEUs could be mapped into 54 to 268 KEGG pathways. The expression of DEUs related to insecticide metabolism related genes were analyzed. In the insecticide metabolism related genes cuticle protein is the largest group in DEUs and the second largest is ABC transporter. Our study will facilitate molecular research on insecticide resistance in S. avenae as well as in other wheat aphids.	miR 430 / embryos were injected with miR 430 rescued 20 embryos at shield stage were collected for RNA seq analsysis	Rescued	R6	strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:Hong Kong\|age:6 hpf stage:shield stage\|sex:pooled male and female\|tissue:embyos\|phenotype:MiR 430 / \|sample type:embryos\|treatment:Rescued by miR 430 injection\|BioSampleModel:Model organism or animal	Transcriptome analysis and identification of insecticidemetabolism related genes post exposure to insecticide in Sitobion avenae	IM15min 1	IM15min 1	IM15min 1	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP193814	IM15min_1_S91_L004_R1_001.fastq.gz IM15min_1_S91_L004_R2_001.fastq.gz	fastq fastq	5908953744.0	19566072.0	IM15min 1 S91 L004 R1 001.fastq.gz	0:151 1:151	A:1720180168;C:1223518369;G:1218504877;T:1746709378;N:40952	151	151	1720180168	1223518369	1218504877	1746709378	40952	SRX5733571	SRS4646935	SRA879464	Institute of Plant Protection and Agro-Products Safety\|Anhui Academy of Agricultural Sciences	Institute of Plant Protection and Agro-Products Safety	2	0.0	2e-05	0.0	0.0	1.0	0.99995		0.33333	151	151	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-25	Gastrula	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");;