metadata: run_metadata: 21 rows where experiment.library_selection = "PolyA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation

21 rows where experiment.library_selection = "PolyA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Respiratory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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
31909	31909	SRR28763300	SRX24328708	SRS21090012	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG27	replicate name:12\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG27	EG27	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG27_1.fastq.gz EG27_2.fastq.gz	fastq fastq	9468037636.0	31351118.0	EG27 1.fastq.gz	0:151 1:151	A:2645026688;C:2045224768;G:2241526143;T:2536135792;N:124245	151	151	2645026688	2045224768	2241526143	2536135792	124245	SRX24328708	SRS21090012	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.96043	0.95691	0.0549	0.05519	0.8872	0.88791	0.91642	0.32446	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31910	31910	SRR28763301	SRX24328707	SRS21090011	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG25	replicate name:11\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG25	EG25	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG25_1.fastq.gz EG25_2.fastq.gz	fastq fastq	9880334680.0	32716340.0	EG25 1.fastq.gz	0:151 1:151	A:2794566002;C:2119943184;G:2295436572;T:2670257797;N:131125	151	151	2794566002	2119943184	2295436572	2670257797	131125	SRX24328707	SRS21090011	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.9497	0.94855	0.09296	0.09345	0.78577	0.78806	0.81265	0.81736	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31911	31911	SRR28763302	SRX24328706	SRS21090010	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG23	replicate name:10\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG23	EG23	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG23_2.fastq.gz EG23_1.fastq.gz	fastq fastq	9310716776.0	30830188.0	EG23 1.fastq.gz	0:151 1:151	A:2627699193;C:1989736585;G:2183889311;T:2509270699;N:120988	151	151	2627699193	1989736585	2183889311	2509270699	120988	SRX24328706	SRS21090010	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.95963	0.95589	0.06725	0.06923	0.89331	0.89514	0.92653	0.31643	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31912	31912	SRR28763303	SRX24328705	SRS21090009	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG22	replicate name:9\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG22	EG22	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG22_1.fastq.gz EG22_2.fastq.gz	fastq fastq	10098934662.0	33440181.0	EG22 1.fastq.gz	0:151 1:151	A:2849596303;C:2184335632;G:2385398269;T:2679468419;N:136039	151	151	2849596303	2184335632	2385398269	2679468419	136039	SRX24328705	SRS21090009	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.95966	0.95948	0.0597	0.06018	0.87724	0.87811	0.26587	0.30043	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31913	31913	SRR28763304	SRX24328704	SRS21090008	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG21	replicate name:8\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG21	EG21	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG21_2.fastq.gz EG21_1.fastq.gz	fastq fastq	9455903880.0	31310940.0	EG21 1.fastq.gz	0:151 1:151	A:2632664130;C:2047064096;G:2251422835;T:2524625050;N:127769	151	151	2632664130	2047064096	2251422835	2524625050	127769	SRX24328704	SRS21090008	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.94131	0.94159	0.09983	0.09968	0.83422	0.83473	0.81728	0.82964	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31914	31914	SRR28763305	SRX24328703	SRS21090007	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG20	replicate name:7\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG20	EG20	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG20_1.fastq.gz EG20_2.fastq.gz	fastq fastq	10208944504.0	33804452.0	EG20 1.fastq.gz	0:151 1:151	A:2904784539;C:2158820127;G:2293244638;T:2851958707;N:136493	151	151	2904784539	2158820127	2293244638	2851958707	136493	SRX24328703	SRS21090007	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.94799	0.95097	0.07416	0.07223	0.8591	0.86283	0.90914	0.28764	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31916	31916	SRR28763307	SRX24328701	SRS21090005	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG19	replicate name:6\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 14\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG19	EG19	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG19_1.fastq.gz EG19_2.fastq.gz	fastq fastq	10522416880.0	34842440.0	EG19 1.fastq.gz	0:151 1:151	A:2917044076;C:2328452801;G:2444054841;T:2832724906;N:140256	151	151	2917044076	2328452801	2444054841	2832724906	140256	SRX24328701	SRS21090005	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.95399	0.95401	0.07708	0.07832	0.82045	0.82171	0.74083	0.7189	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31917	31917	SRR28763308	SRX24328700	SRS21090004	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG18	replicate name:5\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 08\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG18	EG18	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG18_1.fastq.gz EG18_2.fastq.gz	fastq fastq	8756609894.0	28995397.0	EG18 1.fastq.gz	0:151 1:151	A:2511054564;C:1846539575;G:2028143579;T:2370754969;N:117207	151	151	2511054564	1846539575	2028143579	2370754969	117207	SRX24328700	SRS21090004	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.95603	0.95467	0.07502	0.07425	0.87547	0.87785	0.30779	0.29873	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31918	31918	SRR28763309	SRX24328699	SRS21090003	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG17	replicate name:4\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 08\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG17	EG17	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG17_1.fastq.gz EG17_2.fastq.gz	fastq fastq	10838410050.0	35888775.0	EG17 1.fastq.gz	0:151 1:151	A:3066998431;C:2291161659;G:2523979315;T:2956127087;N:143558	151	151	3066998431	2291161659	2523979315	2956127087	143558	SRX24328699	SRS21090003	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.94102	0.94248	0.10341	0.10249	0.82276	0.82479	0.86198	0.86305	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31919	31919	SRR28763310	SRX24328698	SRS21090002	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG7	replicate name:3\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 02\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG7	EG7	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG7_1.fastq.gz EG7_2.fastq.gz	fastq fastq	10125638408.0	33528604.0	EG7 1.fastq.gz	0:151 1:151	A:2685408022;C:2334564091;G:2564122607;T:2541408208;N:135480	151	151	2685408022	2334564091	2564122607	2541408208	135480	SRX24328698	SRS21090002	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.96855	0.96773	0.05197	0.05213	0.9124	0.91449	0.90093	0.90061	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31920	31920	SRR28763311	SRX24328697	SRS21090001	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG6	replicate name:2\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 02\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG6	EG6	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG6_1.fastq.gz EG6_2.fastq.gz	fastq fastq	8347409256.0	27640428.0	EG6 1.fastq.gz	0:151 1:151	A:2355233426;C:1773374207;G:1954779935;T:2263909727;N:111961	151	151	2355233426	1773374207	1954779935	2263909727	111961	SRX24328697	SRS21090001	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.95759	0.95489	0.06473	0.06571	0.88262	0.88428	0.92671	0.92842	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
31921	31921	SRR28763312	SRX24328696	SRS21090000	SRP503258	PRJNA1102381	Acidification alters anxiety like behaviour and brain gene expression in zebrafish	PRJNA1102381	Other	CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain acidification caused differential expression of genes involved in cytoskeletal organization cellular transport immunity and the visual neural system. In the gills an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.		EG5	replicate name:1\|breed:AB\|age:4 months\|dev stage:adult\|collection date:2021 11 02\|geo loc name:Hong Kong\|sex:not determined\|tissue:gill\|BioSampleModel:Model organism or animal	RNA Seq of 4mpf Danio rerio gill	EG5	EG5	Total RNA was extracted using the RNeasy Micro Kit Qiagen.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP503258	EG5_1.fastq.gz EG5_2.fastq.gz	fastq fastq	10544509086.0	34915593.0	EG5 1.fastq.gz	0:151 1:151	A:2929107857;C:2307092012;G:2499629363;T:2808538620;N:141234	151	151	2929107857	2307092012	2499629363	2808538620	141234	SRX24328696	SRS21090000	SRA1849282	The University of Hong Kong\|School of Biological Sciences	The University of Hong Kong	2	0.94866	0.9474	0.08636	0.08561	0.87545	0.87726	0.20035	0.88059	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-22	Adult	Adult	Gill	Respiratory System
70108	70108	SRR19561928	SRX15614022	SRS13314708	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr27 2	Dr27 2	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:27 replicate 2\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 6 27 2 gill	6 27 2 gill	6 27 2 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6006 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	6-27-2-gill-RNA_R1.fq.gz 6-27-2-gill-RNA_R2.fq.gz	fastq fastq	15500913600.0	51669712.0	6 27 2 gill RNA R1.fq.gz	0:150 1:150	A:4095447151;C:3602140382;G:3656584139;T:4146436009;N:305919	150	150	4095447151	3602140382	3656584139	4146436009	305919	SRX15614022	SRS13314708	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.9293	0.93327	0.07792	0.07755	0.69351	0.70057	0.51318	0.49677	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70115	70115	SRR19561935	SRX15614015	SRS13314715	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr13 3	Dr13 3	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:13 replicate 3\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 41 13 3 gill	41 13 3 gill	41 13 3 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6048 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	41-13-3-gill-RNA_R1.fq.gz 41-13-3-gill-RNA_R2.fq.gz	fastq fastq	7220390100.0	24067967.0	41 13 3 gill RNA R1.fq.gz	0:150 1:150	A:1921586224;C:1668980274;G:1684853249;T:1944846933;N:123420	150	150	1921586224	1668980274	1684853249	1944846933	123420	SRX15614015	SRS13314715	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.925	0.92628	0.0907	0.09092	0.6872	0.69625	0.50732	0.48568	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70121	70121	SRR19561941	SRX15614009	SRS13314714	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr13 2	Dr13 2	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:13 replicate 2\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 36 13 2 gill	36 13 2 gill	36 13 2 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6042 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	36-13-2-gill-RNA_R1.fq.gz 36-13-2-gill-RNA_R2.fq.gz	fastq fastq	7665737400.0	25552458.0	36 13 2 gill RNA R1.fq.gz	0:150 1:150	A:2016541351;C:1797005643;G:1810103967;T:2041936659;N:149780	150	150	2016541351	1797005643	1810103967	2041936659	149780	SRX15614009	SRS13314714	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.93252	0.93866	0.08604	0.08654	0.69059	0.69349	0.50048	0.49744	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70128	70128	SRR19561948	SRX15614002	SRS13314713	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr13 1	Dr13 1	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:13 replicate 1\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 31 13 1 gill	31 13 1 gill	31 13 1 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6036 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	31-13-1-gill-RNA_R1.fq.gz 31-13-1-gill-RNA_R2.fq.gz	fastq fastq	7585917900.0	25286393.0	31 13 1 gill RNA R1.fq.gz	0:150 1:150	A:2014051232;C:1756759053;G:1767708394;T:2047250965;N:148256	150	150	2014051232	1756759053	1767708394	2047250965	148256	SRX15614002	SRS13314713	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.92182	0.92679	0.09269	0.09288	0.68941	0.69365	0.50632	0.49887	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70134	70134	SRR19561954	SRX15613996	SRS13314712	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr18 3	Dr18 3	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:18 replicate 3\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 26 18 3 gill	26 18 3 gill	26 18 3 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6030 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	26-18-3-gill-RNA_R1.fq.gz 26-18-3-gill-RNA_R2.fq.gz	fastq fastq	7439334900.0	24797783.0	26 18 3 gill RNA R1.fq.gz	0:150 1:150	A:1958318506;C:1744878169;G:1748154378;T:1987838580;N:145267	150	150	1958318506	1744878169	1748154378	1987838580	145267	SRX15613996	SRS13314712	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.93062	0.93534	0.08514	0.0852	0.6884	0.69221	0.48492	0.48516	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70141	70141	SRR19561961	SRX15613989	SRS13314711	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr18 2	Dr18 2	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:18 replicate 2\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 21 18 2 gill	21 18 2 gill	21 18 2 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6024 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	21-18-2-gill-RNA_R1.fq.gz 21-18-2-gill-RNA_R2.fq.gz	fastq fastq	7517863500.0	25059545.0	21 18 2 gill RNA R1.fq.gz	0:150 1:150	A:1969417724;C:1766553319;G:1782068790;T:1999678637;N:145030	150	150	1969417724	1766553319	1782068790	1999678637	145030	SRX15613989	SRS13314711	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.93938	0.94224	0.07633	0.07622	0.69347	0.69656	0.50217	0.50412	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70148	70148	SRR19561968	SRX15613982	SRS13314710	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr18 1	Dr18 1	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:18 replicate 1\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 16 18 1 gill	16 18 1 gill	16 18 1 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6018 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	16-18-1-gill-RNA_R1.fq.gz 16-18-1-gill-RNA_R2.fq.gz	fastq fastq	5988825000.0	19962750.0	16 18 1 gill RNA R1.fq.gz	0:150 1:150	A:1602220465;C:1376565952;G:1387172781;T:1622748254;N:117548	150	150	1602220465	1376565952	1387172781	1622748254	117548	SRX15613982	SRS13314710	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.9336	0.93326	0.08606	0.0867	0.68515	0.69351	0.47018	0.50159	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70154	70154	SRR19561974	SRX15613976	SRS13314709	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr27 3	Dr27 3	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:27 replicate 3\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 11 27 3 gill	11 27 3 gill	11 27 3 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6012 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	11-27-3-gill-RNA_R1.fq.gz 11-27-3-gill-RNA_R2.fq.gz	fastq fastq	7311778500.0	24372595.0	11 27 3 gill RNA R1.fq.gz	0:150 1:150	A:1930903739;C:1701742166;G:1720582156;T:1958404786;N:145653	150	150	1930903739	1701742166	1720582156	1958404786	145653	SRX15613976	SRS13314709	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.92776	0.9312	0.0792	0.0784	0.69694	0.70303	0.51502	0.50193	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory System
70158	70158	SRR19561978	SRX15613972	SRS13314707	SRP378802	PRJNA846110	Danio rerio Raw sequence reads	PRJNA846110	Other	Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio	Dr27 1	Dr27 1	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:adult\|sex:female\|tissue:multi tissue\|aliquot:27 replicate 1\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult female 1 27 1 gill	1 27 1 gill	1 27 1 gill	All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6000 illumina platform.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP378802	1-27-1-gill-RNA_R1.fq.gz 1-27-1-gill-RNA_R2.fq.gz	fastq fastq	7040781900.0	23469273.0	1 27 1 gill RNA R1.fq.gz	0:150 1:150	A:1864838359;C:1635702609;G:1651379589;T:1888719652;N:141691	150	150	1864838359	1635702609	1651379589	1888719652	141691	SRX15613972	SRS13314707	SRA1432943	shanghai ocean university\|College of Fisheries and Life Science	shanghai ocean university	2	0.9243	0.93114	0.07624	0.07579	0.69627	0.70067	0.51735	0.50652	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-06-07	Adult	Adult	Gill	Respiratory 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");;