metadata: run_metadata: 15 rows where experiment.library_strategy = "miRNA-Seq" and tissue

15 rows where experiment.library_strategy = "miRNA-Seq" and tissue_curation = "Multi-tissue"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36560	36560	SRR1048073	SRX363298	SRS369337	SRP016132	PRJNA177642	Danio rerio Transcriptome or Gene expression	PRJNA177642	Other	Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.	Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.	Zebrafish pineal gland	Pineal gland		Zebrafish Brain miRNA	Brain miRNA	1	Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al. 2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by …	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016132	ZB_trimmed.fastq	fastq	323899236.0	14781569.0	Brain miRNA run	0:21.91 1:0	A:77705253;C:63882329;G:85902986;T:96383552;N:25116	21	0	77705253	63882329	85902986	96383552	25116	SRX363298	SRS369337	SRA054264	Tel Aviv University	Tel Aviv University	1	0.88754	0.06569	0.96747	0.53358	23	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Israel	2015-07-22	Adult	Adult	Multi-tissue	Multi-system
36561	36561	SRR1048072	SRX363297	SRS369337	SRP016132	PRJNA177642	Danio rerio Transcriptome or Gene expression	PRJNA177642	Other	Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.	Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.	Zebrafish pineal gland	Pineal gland		Zebrafish pineal gland dark miRNA	Pineal gland dark miRNA	1	Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al. 2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by …	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016132	D_trimmed.fastq	fastq	231371620.0	10385264.0	Pineal gland dark miRNA run	0:22.28 1:0	A:61228408;C:44264639;G:58700027;T:67159878;N:18668	22	0	61228408	44264639	58700027	67159878	18668	SRX363297	SRS369337	SRA054264	Tel Aviv University	Tel Aviv University	1	0.84648	0.04467	0.95645	0.79978	22	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Israel	2015-07-22	Adult	Adult	Multi-tissue	Multi-system
36562	36562	SRR1048071	SRX363296	SRS369337	SRP016132	PRJNA177642	Danio rerio Transcriptome or Gene expression	PRJNA177642	Other	Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.	Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.	Zebrafish pineal gland	Pineal gland		Zebrafish pineal gland light miRNA	Pineal gland light miRNA	1	Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al. 2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. post library quality check by …	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP016132	L_trimmed.fastq	fastq	132417471.0	5933638.0	Pineal gland light miRNA run	0:22.32 1:0	A:36017069;C:26569684;G:32546616;T:37273526;N:10576	22	0	36017069	26569684	32546616	37273526	10576	SRX363296	SRS369337	SRA054264	Tel Aviv University	Tel Aviv University	1	0.86427	0.03426	0.95631	0.86509	21	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Israel	2015-07-22	Adult	Adult	Multi-tissue	Multi-system
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

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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");;