metadata: run_metadata: 21 rows where experiment.library_selection = "PCR", tissue_curation = "Multi-tissue" and tissue_curation

21 rows where experiment.library_selection = "PCR", tissue_curation = "Multi-tissue" and tissue_curation_coarse = "Multi-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
59351	59351	SRR11862874	SRX8413250	SRS6725560	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from stressed adult male batchE	library 10 batchE stress	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Stress\|filename:10SMALL GTTTCG L002 R1 001.fastq.gz\|batch:5\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from stressed adult male batchE	10SMALL GTTTCG L002 R1 001.fastq.gz	10SMALL GTTTCG L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	10SMALL_GTTTCG_L002_R1_001.fastq.gz	fastq	610892898.0	9255953.0	10SMALL GTTTCG L002 R1 001.fastq.gz	0:66	A:131858438;C:155399854;G:158242625;T:165382769;N:9212	66		131858438	155399854	158242625	165382769	9212	SRX8413250	SRS6725560	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.07236		0.0163		0.95574		0.71914		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59352	59352	SRR11862875	SRX8413249	SRS6725559	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from control adult male batchE	library 9 batchE control	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Control\|filename:9SMALL GTGGCC L002 R1 001.fastq.gz\|batch:5\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from control adult male batchE	9SMALL GTGGCC L002 R1 001.fastq.gz	9SMALL GTGGCC L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	9SMALL_GTGGCC_L002_R1_001.fastq.gz	fastq	681019152.0	10318472.0	9SMALL GTGGCC L002 R1 001.fastq.gz	0:66	A:145919628;C:180332988;G:185160654;T:169595863;N:10019	66		145919628	180332988	185160654	169595863	10019	SRX8413249	SRS6725559	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.03361		0.00721		0.97585		0.72421		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59353	59353	SRR11862876	SRX8413248	SRS6725558	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from stressed adult male batchD	library 8 batchD stress	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Stress\|filename:8SMALL GTGAAA L002 R1 001.fastq.gz\|batch:4\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from stressed adult male batchD	8SMALL GTGAAA L002 R1 001.fastq.gz	8SMALL GTGAAA L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	8SMALL_GTGAAA_L002_R1_001.fastq.gz	fastq	881814912.0	13360832.0	8SMALL GTGAAA L002 R1 001.fastq.gz	0:66	A:223839245;C:210712788;G:239626812;T:207623100;N:12967	66		223839245	210712788	239626812	207623100	12967	SRX8413248	SRS6725558	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.01456		0.00285		0.98685		0.79954		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59354	59354	SRR11862877	SRX8413247	SRS6725557	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from control adult male batchD	library 7 batchD control	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Control\|filename:7SMALL GTCCGC L002 R1 001.fastq.gz\|batch:4\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from control adult male batchD	7SMALL GTCCGC L002 R1 001.fastq.gz	7SMALL GTCCGC L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	7SMALL_GTCCGC_L002_R1_001.fastq.gz	fastq	871937682.0	13211177.0	7SMALL GTCCGC L002 R1 001.fastq.gz	0:66	A:187309754;C:240910478;G:236157154;T:207547961;N:12335	66		187309754	240910478	236157154	207547961	12335	SRX8413247	SRS6725557	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.00388		0.00062		0.99622		0.86525		66		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59355	59355	SRR11862878	SRX8413246	SRS6725556	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from stressed adult male batchC	library 6 batchC stress	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Stress\|filename:6SMALL GTAGAG L002 R1 001.fastq.gz\|batch:3\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from stressed adult male batchC	6SMALL GTAGAG L002 R1 001.fastq.gz	6SMALL GTAGAG L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	6SMALL_GTAGAG_L002_R1_001.fastq.gz	fastq	588357594.0	8914509.0	6SMALL GTAGAG L002 R1 001.fastq.gz	0:66	A:138378307;C:145942814;G:162208729;T:141818898;N:8846	66		138378307	145942814	162208729	141818898	8846	SRX8413246	SRS6725556	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.02473		0.00511		0.98317		0.76412		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59356	59356	SRR11862879	SRX8413245	SRS6725555	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from control adult male batchC	library 5 batchC control	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Control\|filename:5SMALL CCGTCC L002 R1 001.fastq.gz\|batch:3\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from control adult male batchC	5SMALL CCGTCC L002 R1 001.fastq.gz	5SMALL CCGTCC L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	5SMALL_CCGTCC_L002_R1_001.fastq.gz	fastq	724072008.0	10970788.0	5SMALL CCGTCC L002 R1 001.fastq.gz	0:66	A:153195532;C:210035381;G:176169980;T:184660888;N:10227	66		153195532	210035381	176169980	184660888	10227	SRX8413245	SRS6725555	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.02036		0.00355		0.98265		0.71654		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59357	59357	SRR11862880	SRX8413244	SRS6725554	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from stressed adult male batchB	library 4 batchB stress	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Stress\|filename:4SMALL ATGTCA L002 R1 001.fastq.gz\|batch:2\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from stressed adult male batchB	4SMALL ATGTCA L002 R1 001.fastq.gz	4SMALL ATGTCA L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	4SMALL_ATGTCA_L002_R1_001.fastq.gz	fastq	734716818.0	11132073.0	4SMALL ATGTCA L002 R1 001.fastq.gz	0:66	A:176688644;C:183414624;G:192032878;T:182569784;N:10888	66		176688644	183414624	192032878	182569784	10888	SRX8413244	SRS6725554	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.03816		0.00665		0.97378		0.80915		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59358	59358	SRR11862881	SRX8413243	SRS6725553	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from control adult male batchB	library 3 batchB control	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Control\|filename:3SMALL AGTTCC L002 R1 001.fastq.gz\|batch:2\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from control adult male batchB	3SMALL AGTTCC L002 R1 001.fastq.gz	3SMALL AGTTCC L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	3SMALL_AGTTCC_L002_R1_001.fastq.gz	fastq	639608178.0	9691033.0	3SMALL AGTTCC L002 R1 001.fastq.gz	0:66	A:141927022;C:169937693;G:166391833;T:161342157;N:9473	66		141927022	169937693	166391833	161342157	9473	SRX8413243	SRS6725553	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.00358		0.00027		0.99857		0.92025		66		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59359	59359	SRR11862882	SRX8413242	SRS6725552	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from stressed adult male batchF	library 12 batchF stress	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Stress\|filename:12SMALL GAGTGG L002 R1 001.fastq.gz\|batch:6\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from stressed adult male batchF	12SMALL GAGTGG L002 R1 001.fastq.gz	12SMALL GAGTGG L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	12SMALL_GAGTGG_L002_R1_001.fastq.gz	fastq	856789890.0	12981665.0	12SMALL GAGTGG L002 R1 001.fastq.gz	0:66	A:197687950;C:209840385;G:245135169;T:204114009;N:12377	66		197687950	209840385	245135169	204114009	12377	SRX8413242	SRS6725552	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.13729		0.02049		0.93752		0.71536		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59360	59360	SRR11862883	SRX8413241	SRS6725551	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from control adult male batchF	library 11 batchF control	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Control\|filename:11SMALL CGTACG L002 R1 001.fastq.gz\|batch:6\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from control adult male batchF	11SMALL CGTACG L002 R1 001.fastq.gz	11SMALL CGTACG L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	11SMALL_CGTACG_L002_R1_001.fastq.gz	fastq	891015576.0	13500236.0	11SMALL CGTACG L002 R1 001.fastq.gz	0:66	A:215219357;C:226988408;G:230348786;T:218445888;N:13137	66		215219357	226988408	230348786	218445888	13137	SRX8413241	SRS6725551	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.10021		0.02466		0.95789		0.65844		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59361	59361	SRR11862884	SRX8413240	SRS6725550	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from stressed adult male batchA	library 2 batchA stress	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Stress\|filename:2SMALL AGTCAA L002 R1 001.fastq.gz\|batch:1\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from stressed adult male batchA	2SMALL AGTCAA L002 R1 001.fastq.gz	2SMALL AGTCAA L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	2SMALL_AGTCAA_L002_R1_001.fastq.gz	fastq	790770684.0	11981374.0	2SMALL AGTCAA L002 R1 001.fastq.gz	0:66	A:198694732;C:195900186;G:206731529;T:189432489;N:11748	66		198694732	195900186	206731529	189432489	11748	SRX8413240	SRS6725550	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.06132		0.01001		0.96731		0.807		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
59362	59362	SRR11862885	SRX8413239	SRS6725549	SRP265077	PRJNA635603	Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs	PRJNA635603	Other	A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm which may in turn have influenced offspring development.	Small RNA seq of zebrafish spermatozoa from control adult male batchA	library 1 batchA control	strain:London Wildtype\|dev stage:Adult\|sex:male\|tissue:not applicable\|cell type:Spermatozoa\|geo loc name:United Kingdom: Sheffield\|treatment:Control\|filename:1SMALL CTTGTA L002 R1 001.fastq.gz\|batch:1\|BioSampleModel:Model organism or animal	Small RNA seq of zebrafish spermatozoa from control adult male batchA	1SMALL CTTGTA L002 R1 001.fastq.gz	1SMALL CTTGTA L002 R1 001.fastq.gz	Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure periodic net chasing or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS pelleted 1000 xg for 10 mins re suspended in Tri reagent and stored at 80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at 20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ…	miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP265077	1SMALL_CTTGTA_L002_R1_001.fastq.gz	fastq	796394940.0	12066590.0	1SMALL CTTGTA L002 R1 001.fastq.gz	0:66	A:180861950;C:199407609;G:204723388;T:211390521;N:11472	66		180861950	199407609	204723388	211390521	11472	SRX8413239	SRS6725549	SRA1080712	University of Tartu\|Department of Pathophysiology	University of Tartu	1	0.01922		0.00235		0.99024		0.87449		66		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Estonia	2020-05-28	Adult	Adult	Multi-tissue	Multi-system
64970	64970	SRR14999363	SRX11311655	SRS9340853	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	L 1	L 1	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =L 1\|BioSampleModel:Model organism or animal	L 1	FRAS210007515 1r	FRAS210007515 1r	0.8g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	L_96h_1_1.fq.gz L_96h_1_2.fq.gz	fastq fastq	6019278600.0	20064262.0	L 96h 1 1.fq.gz	0:150 1:150	A:1581092490;C:1430552191;G:1435208634;T:1572284027;N:141258	150	150	1581092490	1430552191	1435208634	1572284027	141258	SRX11311655	SRS9340853	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.94261	0.9417	0.02923	0.02882	0.7051	0.70725	0.48809	0.49074	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64971	64971	SRR14999364	SRX11311654	SRS9340852	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	C 3	C 3	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =C 3\|BioSampleModel:Model organism or animal	C 3	FRAS210007514 3r	FRAS210007514 3r	0g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	C_96h_3_1.fq.gz C_96h_3_2.fq.gz	fastq fastq	6857670600.0	22858902.0	C 96h 3 1.fq.gz	0:150 1:150	A:1841430105;C:1590688013;G:1597543269;T:1827853044;N:156169	150	150	1841430105	1590688013	1597543269	1827853044	156169	SRX11311654	SRS9340852	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.93924	0.93826	0.0592	0.05873	0.65673	0.65766	0.49758	0.50371	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64972	64972	SRR14999365	SRX11311653	SRS9340851	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	C 2	C 2	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =C 2\|BioSampleModel:Model organism or animal	C 2	FRAS210007514 2r	FRAS210007514 2r	0g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	C_96h_2_1.fq.gz C_96h_2_2.fq.gz	fastq fastq	6348703200.0	21162344.0	C 96h 2 1.fq.gz	0:150 1:150	A:1700541402;C:1478742180;G:1481199683;T:1688070707;N:149228	150	150	1700541402	1478742180	1481199683	1688070707	149228	SRX11311653	SRS9340851	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.94135	0.94114	0.05775	0.0572	0.66101	0.66265	0.50778	0.50788	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64973	64973	SRR14999366	SRX11311652	SRS9340850	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	C 1	C 1	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|cultivar:not collected\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =C 1\|BioSampleModel:Model organism or animal	C 1	FRAS210007514 1r	FRAS210007514 1r	0g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	C_96h_1_1.fq.gz C_96h_1_2.fq.gz	fastq fastq	6463471200.0	21544904.0	C 96h 1 1.fq.gz	0:150 1:150	A:1733784762;C:1501594175;G:1506005187;T:1721935805;N:151271	150	150	1733784762	1501594175	1506005187	1721935805	151271	SRX11311652	SRS9340850	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.93808	0.93829	0.05961	0.05918	0.65884	0.65873	0.50462	0.50091	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64974	64974	SRR14999367	SRX11311651	SRS9340849	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	H 3	H 3	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =H 3\|BioSampleModel:Model organism or animal	H 3	FRAS210007516 3r	FRAS210007516 3r	2.0g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	H_96h_3_1.fq.gz H_96h_3_2.fq.gz	fastq fastq	5638058700.0	18793529.0	H 96h 3 1.fq.gz	0:150 1:150	A:1495034040;C:1330177281;G:1330682910;T:1482034263;N:130206	150	150	1495034040	1330177281	1330682910	1482034263	130206	SRX11311651	SRS9340849	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.93535	0.93491	0.02553	0.02529	0.72456	0.72474	0.50213	0.49962	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64975	64975	SRR14999368	SRX11311650	SRS9340848	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	H 2	H 2	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =H 2\|BioSampleModel:Model organism or animal	H 2	FRAS210007516 2r	FRAS210007516 2r	2.0g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	H_96h_2_1.fq.gz H_96h_2_2.fq.gz	fastq fastq	6161230800.0	20537436.0	H 96h 2 1.fq.gz	0:150 1:150	A:1637006263;C:1449880253;G:1451565756;T:1622634286;N:144242	150	150	1637006263	1449880253	1451565756	1622634286	144242	SRX11311650	SRS9340848	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.93477	0.93452	0.02553	0.02539	0.72395	0.72494	0.49506	0.49921	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64976	64976	SRR14999369	SRX11311649	SRS9340847	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	H 1	H 1	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate=H 1\|BioSampleModel:Model organism or animal	H 1	FRAS210007516 1r	FRAS210007516 1r	2.0g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	H_96h_1_1.fq.gz H_96h_1_2.fq.gz	fastq fastq	6624273900.0	22080913.0	H 96h 1 1.fq.gz	0:150 1:150	A:1755735186;C:1561147696;G:1566612960;T:1740622508;N:155550	150	150	1755735186	1561147696	1566612960	1740622508	155550	SRX11311649	SRS9340847	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.93425	0.93322	0.0254	0.0252	0.72606	0.72669	0.50622	0.50832	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64977	64977	SRR14999370	SRX11311648	SRS9340845	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	L 3	L 3	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =L 3\|BioSampleModel:Model organism or animal	L 3	FRAS210007515 3r	FRAS210007515 3r	0.8g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	L_96h_3_1.fq.gz L_96h_3_2.fq.gz	fastq fastq	6466250400.0	21554168.0	L 96h 3 1.fq.gz	0:150 1:150	A:1702486578;C:1534421173;G:1535282758;T:1693909718;N:150173	150	150	1702486578	1534421173	1535282758	1693909718	150173	SRX11311648	SRS9340845	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.94324	0.94217	0.03039	0.02989	0.70278	0.70418	0.49161	0.49083	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system
64978	64978	SRR14999371	SRX11311647	SRS9340846	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.	L 2	L 2	strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =L 2\|BioSampleModel:Model organism or animal	L 2	FRAS210007515 2r	FRAS210007515 2r	0.8g/L;h=96h;zebrafish	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP324442	L_96h_2_1.fq.gz L_96h_2_2.fq.gz	fastq fastq	6804970800.0	22683236.0	L 96h 2 1.fq.gz	0:150 1:150	A:1788345091;C:1614590700;G:1621811406;T:1780069163;N:154440	150	150	1788345091	1614590700	1621811406	1780069163	154440	SRX11311647	SRS9340846	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.94141	0.94045	0.03027	0.0302	0.70207	0.70234	0.48625	0.48905	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system

Advanced export

JSON shape: default, array, newline-delimited

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");;