metadata: run_metadata: 12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "size fractionation" and experiment.platform = "ABI

12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "size fractionation" and experiment.platform = "ABI_SOLID"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.library_name	experiment.design_description	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	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
36482	36482	SRR530894	SRX172598	SRS352620	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	60hpf TCDD 3	GSM979608	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:TCDD	60hpf TCDD 3	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:TCDD	GSM979608	GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq	GSM979608 1	GSM979608: 60hpf TCDD 3	1	GEO Accession:GSM979608	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646			1007239870.0	28778282.0	GSM979608 r1	0:35	0:284531587;1:248579138;2:213782485;3:258771962;.:1574698	35	SRX172598	SRS352620	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.04824	0.03	0.981	0.49967	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Hatching	Embryo	Embryo Imprecise	All anatomical structures
36483	36483	SRR530893	SRX172597	SRS352619	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	60hpf TCDD 2	GSM979607	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:TCDD	60hpf TCDD 2	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:TCDD	GSM979607	GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq	GSM979607 1	GSM979607: 60hpf TCDD 2	1	GEO Accession:GSM979607	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0011.csfasta	SOLiD_native	407347325.0	11638495.0	GSM979607 r1	0:35	0:99062820;1:113921998;2:81336108;3:112422342;.:604057	35	SRX172597	SRS352619	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.04258	0.02455	0.98287	0.5048	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Hatching	Embryo	Embryo Imprecise	All anatomical structures
36484	36484	SRR530892	SRX172596	SRS352618	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	60hpf TCDD 1	GSM979606	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:TCDD	60hpf TCDD 1	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:TCDD	GSM979606	GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq	GSM979606 1	GSM979606: 60hpf TCDD 1	1	GEO Accession:GSM979606	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0010.csfasta	SOLiD_native	680837045.0	19452487.0	GSM979606 r1	0:35	0:165079839;1:167219862;2:147812329;3:199659766;.:1065249	35	SRX172596	SRS352618	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.02295	0.01479	0.98884	0.55191	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Hatching	Embryo	Embryo Imprecise	All anatomical structures
36485	36485	SRR530891	SRX172595	SRS352617	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	60hpf DMSO 3	GSM979605	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:DMSO	60hpf DMSO 3	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:DMSO	GSM979605	GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq	GSM979605 1	GSM979605: 60hpf DMSO 3	1	GEO Accession:GSM979605	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0009.csfasta	SOLiD_native	495019840.0	14143424.0	GSM979605 r1	0:35	0:134854583;1:126192934;2:102458221;3:130747961;.:766141	35	SRX172595	SRS352617	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.06707	0.04409	0.97285	0.5058	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Hatching	Embryo	Embryo Imprecise	All anatomical structures
36486	36486	SRR530890	SRX172594	SRS352616	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	60hpf DMSO 2	GSM979604	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:DMSO	60hpf DMSO 2	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:DMSO	GSM979604	GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq	GSM979604 1	GSM979604: 60hpf DMSO 2	1	GEO Accession:GSM979604	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0008.qual	SOLiD_native	440403425.0	12582955.0	GSM979604 r1	0:35	0:110302240;1:106481197;2:104551283;3:118415637;.:653068	35	SRX172594	SRS352616	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.05778	0.03522	0.97423	0.50884	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Hatching	Embryo	Embryo Imprecise	All anatomical structures
36487	36487	SRR530889	SRX172593	SRS352615	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	60hpf DMSO 1	GSM979603	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:DMSO	60hpf DMSO 1	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:60 hpf\|treatment:DMSO	GSM979603	GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq	GSM979603 1	GSM979603: 60hpf DMSO 1	1	GEO Accession:GSM979603	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0007.csfasta MH_0007.qual	SOLiD_native SOLiD_native	583800490.0	16680014.0	GSM979603 r1	0:35	0:166122108;1:149534173;2:111986455;3:155255262;.:902492	35	SRX172593	SRS352615	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.05644	0.03829	0.9781	0.4997	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Hatching	Embryo	Embryo Imprecise	All anatomical structures
36488	36488	SRR530888	SRX172592	SRS352614	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	36hpf TCDD 3	GSM979602	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:TCDD	36hpf TCDD 3	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:TCDD	GSM979602	GSM979602: 36hpf TCDD 3; Danio rerio; RNA Seq	GSM979602 1	GSM979602: 36hpf TCDD 3	1	GEO Accession:GSM979602	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0006.qual MH_0006.csfasta	SOLiD_native SOLiD_native	214059615.0	6115989.0	GSM979602 r1	0:35	0:56635752;1:54053300;2:48355842;3:54677354;.:337367	35	SRX172592	SRS352614	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.13044	0.07694	0.95704	0.53005	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
36489	36489	SRR530887	SRX172591	SRS352613	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	36hpf TCDD 2	GSM979601	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:TCDD	36hpf TCDD 2	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:TCDD	GSM979601	GSM979601: 36hpf TCDD 2; Danio rerio; RNA Seq	GSM979601 1	GSM979601: 36hpf TCDD 2	1	GEO Accession:GSM979601	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646			388475115.0	11099289.0	GSM979601 r1	0:35	0:103611863;1:99408831;2:86592980;3:98238344;.:623097	35	SRX172591	SRS352613	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.15634	0.10763	0.96069	0.47755	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
36490	36490	SRR530886	SRX172590	SRS352612	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	36hpf TCDD 1	GSM979600	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:TCDD	36hpf TCDD 1	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:TCDD	GSM979600	GSM979600: 36hpf TCDD 1; Danio rerio; RNA Seq	GSM979600 1	GSM979600: 36hpf TCDD 1	1	GEO Accession:GSM979600	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0004.csfasta	SOLiD_native	366389765.0	10468279.0	GSM979600 r1	0:35	0:100797199;1:91391785;2:80412155;3:93217840;.:570786	35	SRX172590	SRS352612	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.14106	0.09874	0.95724	0.49685	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
36491	36491	SRR530885	SRX172589	SRS352611	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	36hpf DMSO 3	GSM979599	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:DMSO	36hpf DMSO 3	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:DMSO	GSM979599	GSM979599: 36hpf DMSO 3; Danio rerio; RNA Seq	GSM979599 1	GSM979599: 36hpf DMSO 3	1	GEO Accession:GSM979599	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0003.csfasta	SOLiD_native	2108864835.0	60253281.0	GSM979599 r1	0:35	0:591489585;1:461028640;2:379338654;3:673048278;.:3959678	35	SRX172589	SRS352611	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.09321	0.06563	0.98244	0.50577	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
36492	36492	SRR530884	SRX172588	SRS352610	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	36hpf DMSO 2	GSM979598	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:DMSO	36hpf DMSO 2	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:DMSO	GSM979598	GSM979598: 36hpf DMSO 2; Danio rerio; RNA Seq	GSM979598 1	GSM979598: 36hpf DMSO 2	1	GEO Accession:GSM979598	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0002.qual	SOLiD_native	363765885.0	10393311.0	GSM979598 r1	0:35	0:99316622;1:92947128;2:80099367;3:90839592;.:563176	35	SRX172588	SRS352610	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.13435	0.09839	0.96146	0.49914	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
36493	36493	SRR530883	SRX172587	SRS352609	SRP014646	PRJNA171751	MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]	GSE39808	Transcriptome Analysis	Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing	parent bioproject:PRJNA171747	pubmed:22921993	36hpf DMSO 1	GSM979597	source name:Embryos\|strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:DMSO	36hpf DMSO 1	CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files	Embryos	Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.	strain:TL wild type\|tissue:embryos\|time:36 hpf\|treatment:DMSO	GSM979597	GSM979597: 36hpf DMSO 1; Danio rerio; RNA Seq	GSM979597 1	GSM979597: 36hpf DMSO 1	1	GEO Accession:GSM979597	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014646	MH_0001F3.csfasta MH_0001F3_QV.qual	SOLiD_native SOLiD_native	309659000.0	8847400.0	GSM979597 r1	0:35	0:83729307;1:78100521;2:70827559;3:76531823;.:469790	35	SRX172587	SRS352609	SRA056525	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.56398	0.33182	0.91092	0.5842	35	B	usable mapping rate	legacy	early	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2012-08-01	Pharyngula	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");;