metadata: run_metadata: 281 rows where experiment.library_selection = "size fractionation" and experiment.library

281 rows where experiment.library_selection = "size fractionation" and experiment.library_strategy = "miRNA-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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
37991	37991	SRR1265766	SRX529160	SRS598857	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Heart Replicate 3 sRNAseq	GSM1376649	source name:Heart\|tissue:Heart\|genetic background:Wild type Singapore strain	Heart Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Heart	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Heart\|genetic background:Wild type Singapore strain	GSM1376649	GSM1376649: Heart Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376649		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376649	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZH008_GATCAG_L005_R1.fastq.gz	fastq	4401229692.0	57910917.0	GSM1376649 r1	0:76	A:1009381958;C:1130057881;G:1173217392;T:1088123982;N:448479	76		1009381958	1130057881	1173217392	1088123982	448479	SRX529160	SRS598857	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00129	0.00046	0.99882	0.51351	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Heart	Cardiovascular System
37992	37992	SRR1265765	SRX529159	SRS598856	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Heart Replicate 2 sRNAseq	GSM1376648	source name:Heart\|tissue:Heart\|genetic background:Wild type Singapore strain	Heart Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Heart	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Heart\|genetic background:Wild type Singapore strain	GSM1376648	GSM1376648: Heart Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376648		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376648	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZH007_ACTTGA_L005_R1.fastq.gz	fastq	3202357508.0	42136283.0	GSM1376648 r1	0:76	A:666309720;C:845347679;G:846066601;T:844306103;N:327405	76		666309720	845347679	846066601	844306103	327405	SRX529159	SRS598856	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00042	3e-05	0.99924	0.56521	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Heart	Cardiovascular System
37993	37993	SRR1265764	SRX529158	SRS598855	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Heart Replicate 1 sRNAseq	GSM1376647	source name:Heart\|tissue:Heart\|genetic background:Wild type Singapore strain	Heart Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Heart	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Heart\|genetic background:Wild type Singapore strain	GSM1376647	GSM1376647: Heart Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376647		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376647	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZH002_CAGATC_L005_R1.fastq.gz	fastq	3777814232.0	49708082.0	GSM1376647 r1	0:76	A:791204432;C:1050679958;G:1001897360;T:933655799;N:376683	76		791204432	1050679958	1001897360	933655799	376683	SRX529158	SRS598855	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00034	4e-05	0.99943	0.62264	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Heart	Cardiovascular System
37994	37994	SRR1265763	SRX529157	SRS598854	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Eye Replicate 3 sRNAseq	GSM1376646	source name:Eye\|tissue:Eye\|genetic background:Wild type Singapore strain	Eye Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Eye	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Eye\|genetic background:Wild type Singapore strain	GSM1376646	GSM1376646: Eye Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376646		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376646	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZE014_GCCAAT_L005_R1.fastq.gz	fastq	299134784.0	3935984.0	GSM1376646 r1	0:76	A:62089027;C:82689882;G:78294122;T:76032871;N:28882	76		62089027	82689882	78294122	76032871	28882	SRX529157	SRS598854	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00078	8e-05	0.99892	0.66406	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Eye	Sensory System
37995	37995	SRR1265762	SRX529156	SRS598853	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Eye Replicate 2 sRNAseq	GSM1376645	source name:Eye\|tissue:Eye\|genetic background:Wild type Singapore strain	Eye Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Eye	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Eye\|genetic background:Wild type Singapore strain	GSM1376645	GSM1376645: Eye Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376645		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376645	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZE013_ACAGTG_L005_R1.fastq.gz	fastq	622465080.0	8190330.0	GSM1376645 r1	0:76	A:127621827;C:166524813;G:172833628;T:155425094;N:59718	76		127621827	166524813	172833628	155425094	59718	SRX529156	SRS598853	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00132	7e-05	0.99886	0.66956	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Eye	Sensory System
37996	37996	SRR1265761	SRX529155	SRS598852	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Eye Replicate 1 sRNAseq	GSM1376644	source name:Eye\|tissue:Eye\|genetic background:Wild type Singapore strain	Eye Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Eye	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Eye\|genetic background:Wild type Singapore strain	GSM1376644	GSM1376644: Eye Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376644		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376644	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZE008_TGACCA_L005_R1.fastq.gz	fastq	906617148.0	11929173.0	GSM1376644 r1	0:76	A:188700519;C:246755919;G:238402849;T:232669963;N:87898	76		188700519	246755919	238402849	232669963	87898	SRX529155	SRS598852	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00073	4e-05	0.9991	0.61788	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Eye	Sensory System
37997	37997	SRR1265760	SRX529154	SRS598851	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Testis Replicate 3 sRNAseq	GSM1376643	source name:Testis\|gender:male\|tissue:Testis\|genetic background:Wild type Singapore strain	Testis Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Testis	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Testis\|genetic background:Wild type Singapore strain	GSM1376643	GSM1376643: Testis Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376643		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376643	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZT004_GCCAAT_L004_R1.fastq.gz	fastq	1096387628.0	14426153.0	GSM1376643 r1	0:76	A:268706118;C:286539627;G:262643519;T:278353167;N:145197	76		268706118	286539627	262643519	278353167	145197	SRX529154	SRS598851	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00659	0.00333	0.99845	0.7331	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
37998	37998	SRR1265759	SRX529153	SRS598850	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Testis Replicate 2 sRNAseq	GSM1376642	source name:Testis\|gender:male\|tissue:Testis\|genetic background:Wild type Singapore strain	Testis Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Testis	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Testis\|genetic background:Wild type Singapore strain	GSM1376642	GSM1376642: Testis Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376642		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376642	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZT003_ACAGTG_L004_R1.fastq.gz	fastq	1562745896.0	20562446.0	GSM1376642 r1	0:76	A:381752411;C:387452090;G:395892335;T:397438930;N:210130	76		381752411	387452090	395892335	397438930	210130	SRX529153	SRS598850	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01222	0.00651	0.99788	0.69591	76	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
37999	37999	SRR1265758	SRX529152	SRS598849	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Testis Replicate 1 sRNAseq	GSM1376641	source name:Testis\|gender:male\|tissue:Testis\|genetic background:Wild type Singapore strain	Testis Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Testis	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Testis\|genetic background:Wild type Singapore strain	GSM1376641	GSM1376641: Testis Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376641		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376641	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZT001_TGACCA_L004_R1.fastq.gz	fastq	1368892316.0	18011741.0	GSM1376641 r1	0:76	A:335715713;C:358829703;G:326742789;T:347419137;N:184974	76		335715713	358829703	326742789	347419137	184974	SRX529152	SRS598849	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00032	3e-05	0.99943	0.69387	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38000	38000	SRR1265757	SRX529151	SRS598848	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Ovary Replicate 3 sRNAseq	GSM1376640	source name:Ovary\|gender:female\|tissue:Ovary\|genetic background:Wild type Singapore strain	Ovary Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Ovary	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Ovary\|genetic background:Wild type Singapore strain	GSM1376640	GSM1376640: Ovary Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376640		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376640	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZO006_GATCAG_L008_R1.fastq.gz	fastq	1411005984.0	27666784.0	GSM1376640 r1	0:51	A:326542153;C:314421825;G:411019622;T:358847379;N:175005	51		326542153	314421825	411019622	358847379	175005	SRX529151	SRS598848	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00638	0.00068	0.99513	0.75483	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38001	38001	SRR1265756	SRX529150	SRS598847	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Ovary Replicate 2 sRNAseq	GSM1376639	source name:Ovary\|gender:female\|tissue:Ovary\|genetic background:Wild type Singapore strain	Ovary Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Ovary	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Ovary\|genetic background:Wild type Singapore strain	GSM1376639	GSM1376639: Ovary Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376639		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376639	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZO005_ACTTGA_L008_R1.fastq.gz	fastq	765419424.0	15008224.0	GSM1376639 r1	0:51	A:179455664;C:170237021;G:221342071;T:194287721;N:96947	51		179455664	170237021	221342071	194287721	96947	SRX529150	SRS598847	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.02512	0.00355	0.98212	0.67744	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38002	38002	SRR1265755	SRX529149	SRS598846	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Ovary Replicate 1 sRNAseq	GSM1376638	source name:Ovary\|gender:female\|tissue:Ovary\|genetic background:Wild type Singapore strain	Ovary Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Ovary	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Ovary\|genetic background:Wild type Singapore strain	GSM1376638	GSM1376638: Ovary Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376638		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376638	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZO004_CAGATC_L008_R1.fastq.gz	fastq	487558674.0	9559974.0	GSM1376638 r1	0:51	A:114833813;C:108951811;G:140408702;T:123302557;N:61791	51		114833813	108951811	140408702	123302557	61791	SRX529149	SRS598846	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00298	0.0004	0.99644	0.84584	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38003	38003	SRR1265754	SRX529148	SRS598845	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Liver Replicate 3 sRNAseq	GSM1376637	source name:Female Liver\|gender:female\|tissue:Liver\|genetic background:Wild type Singapore strain	Female Liver Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Liver	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Liver\|genetic background:Wild type Singapore strain	GSM1376637	GSM1376637: Female Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376637		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376637	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZL012_GCCAAT_L008_R1.fastq.gz	fastq	105717543.0	2072893.0	GSM1376637 r1	0:51	A:22408978;C:25732405;G:31681641;T:25880225;N:14294	51		22408978	25732405	31681641	25880225	14294	SRX529148	SRS598845	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.05572	0.0017	0.99691	0.56539	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Liver	Liver and Biliary System
38004	38004	SRR1265753	SRX529147	SRS598844	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Liver Replicate 2 sRNAseq	GSM1376636	source name:Female Liver\|gender:female\|tissue:Liver\|genetic background:Wild type Singapore strain	Female Liver Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Liver	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Liver\|genetic background:Wild type Singapore strain	GSM1376636	GSM1376636: Female Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376636		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376636	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZL011_ACAGTG_L008_R1.fastq.gz	fastq	484614546.0	9502246.0	GSM1376636 r1	0:51	A:98373224;C:113894197;G:148444486;T:123841427;N:61212	51		98373224	113894197	148444486	123841427	61212	SRX529147	SRS598844	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01517	0.00112	0.9964	0.61558	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Liver	Liver and Biliary System
38005	38005	SRR1265752	SRX529146	SRS598843	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Liver Replicate 1 sRNAseq	GSM1376635	source name:Female Liver\|gender:female\|tissue:Liver\|genetic background:Wild type Singapore strain	Female Liver Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Liver	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Liver\|genetic background:Wild type Singapore strain	GSM1376635	GSM1376635: Female Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376635		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376635	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZL010_TGACCA_L008_R1.fastq.gz	fastq	304949706.0	5979406.0	GSM1376635 r1	0:51	A:62732698;C:71083849;G:92267430;T:78825237;N:40492	51		62732698	71083849	92267430	78825237	40492	SRX529146	SRS598843	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01218	0.001	0.99709	0.55264	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Liver	Liver and Biliary System
38006	38006	SRR1265751	SRX529145	SRS598842	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Liver Replicate 3 sRNAseq	GSM1376634	source name:Male Liver\|gender:male\|tissue:Liver\|genetic background:Wild type Singapore strain	Male Liver Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Liver	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Liver\|genetic background:Wild type Singapore strain	GSM1376634	GSM1376634: Male Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376634		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376634	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZL009_GATCAG_L007_R1.fastq.gz	fastq	287383266.0	5634966.0	GSM1376634 r1	0:51	A:54829818;C:73200212;G:89994996;T:69332773;N:25467	51		54829818	73200212	89994996	69332773	25467	SRX529145	SRS598842	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00273	0.00026	0.99791	0.69537	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Liver	Liver and Biliary System
38007	38007	SRR1265750	SRX529144	SRS598841	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Liver Replicate 2 sRNAseq	GSM1376633	source name:Male Liver\|gender:male\|tissue:Liver\|genetic background:Wild type Singapore strain	Male Liver Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Liver	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Liver\|genetic background:Wild type Singapore strain	GSM1376633	GSM1376633: Male Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376633		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376633	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZL008_ACTTGA_L007_R1.fastq.gz	fastq	595761753.0	11681603.0	GSM1376633 r1	0:51	A:111507488;C:155297338;G:186229891;T:142672923;N:54113	51		111507488	155297338	186229891	142672923	54113	SRX529144	SRS598841	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00597	0.00067	0.99679	0.72807	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Liver	Liver and Biliary System
38008	38008	SRR1265749	SRX529143	SRS598840	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Liver Replicate 1 sRNAseq	GSM1376632	source name:Male Liver\|gender:male\|tissue:Liver\|genetic background:Wild type Singapore strain	Male Liver Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Liver	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Liver\|genetic background:Wild type Singapore strain	GSM1376632	GSM1376632: Male Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376632		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376632	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZL007_CAGATC_L007_R1.fastq.gz	fastq	976402599.0	19145149.0	GSM1376632 r1										SRX529143	SRS598840	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00348	0.00035	0.99742	0.69292	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Liver	Liver and Biliary System
38009	38009	SRR1265748	SRX529142	SRS598839	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Gut Replicate 3 sRNAseq	GSM1376631	source name:Female Gut\|gender:female\|tissue:Gut\|genetic background:Wild type Singapore strain	Female Gut Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Gut	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Gut\|genetic background:Wild type Singapore strain	GSM1376631	GSM1376631: Female Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376631		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376631	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZG012_TTAGGC_L008_R1.fastq.gz	fastq	425902173.0	8351023.0	GSM1376631 r1	0:51	A:85733692;C:98728458;G:130104130;T:111282282;N:53611	51		85733692	98728458	130104130	111282282	53611	SRX529142	SRS598839	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00598	0.00074	0.99565	0.68818	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gut	Digestive System
38010	38010	SRR1265747	SRX529141	SRS598838	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Gut Replicate 2 sRNAseq	GSM1376630	source name:Female Gut\|gender:female\|tissue:Gut\|genetic background:Wild type Singapore strain	Female Gut Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Gut	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Gut\|genetic background:Wild type Singapore strain	GSM1376630	GSM1376630: Female Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376630		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376630	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZG011_CGATGT_L008_R1.fastq.gz	fastq	464997192.0	9117592.0	GSM1376630 r1	0:51	A:94817360;C:107530735;G:141688278;T:120903676;N:57143	51		94817360	107530735	141688278	120903676	57143	SRX529141	SRS598838	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00297	0.00033	0.9975	0.62721	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gut	Digestive System
38011	38011	SRR1265746	SRX529140	SRS598837	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Gut Replicate 1 sRNAseq	GSM1376629	source name:Female Gut\|gender:female\|tissue:Gut\|genetic background:Wild type Singapore strain	Female Gut Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Gut	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Gut\|genetic background:Wild type Singapore strain	GSM1376629	GSM1376629: Female Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376629		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376629	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZG010_ATCACG_L008_R1.fastq.gz	fastq	798808308.0	15662908.0	GSM1376629 r1	0:51	A:163944400;C:183125028;G:240040726;T:211597768;N:100386	51		163944400	183125028	240040726	211597768	100386	SRX529140	SRS598837	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01106	0.00122	0.99466	0.66862	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gut	Digestive System
38012	38012	SRR1265745	SRX529139	SRS598836	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Gut Replicate 3 sRNAseq	GSM1376628	source name:Male Gut\|gender:male\|tissue:Gut\|genetic background:Wild type Singapore strain	Male Gut Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Gut	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Gut\|genetic background:Wild type Singapore strain	GSM1376628	GSM1376628: Male Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376628		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376628	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZG009_GCCAAT_L007_R1.fastq.gz	fastq	224291778.0	4397878.0	GSM1376628 r1	0:51	A:45043664;C:58692343;G:66840019;T:53695301;N:20451	51		45043664	58692343	66840019	53695301	20451	SRX529139	SRS598836	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.0015	0.00021	0.99829	0.69477	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gut	Digestive System
38013	38013	SRR1265743	SRX529138	SRS598835	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Gut Replicate 1 sRNAseq	GSM1376626	source name:Male Gut\|gender:male\|tissue:Gut\|genetic background:Wild type Singapore strain	Male Gut Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Gut	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Gut\|genetic background:Wild type Singapore strain	GSM1376626	GSM1376626: Male Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376626		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376626	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZG007_TGACCA_L007_R1.fastq.gz	fastq	1058961552.0	20763952.0	GSM1376626 r1	0:51	A:205056709;C:273349362;G:322710601;T:257753257;N:91623	51		205056709	273349362	322710601	257753257	91623	SRX529138	SRS598835	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00382	0.00043	0.99746	0.683	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gut	Digestive System
38014	38014	SRR1265742	SRX529137	SRS598834	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Brain Replicate 3 sRNAseq	GSM1376625	source name:Female Brain\|gender:female\|tissue:Brain\|genetic background:Wild type Singapore strain	Female Brain Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Brain	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Brain\|genetic background:Wild type Singapore strain	GSM1376625	GSM1376625: Female Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376625		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376625	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZB012_CTTGTA_L007_R1.fastq.gz	fastq	657620928.0	12894528.0	GSM1376625 r1	0:51	A:127428594;C:157315630;G:203096060;T:169719399;N:61245	51		127428594	157315630	203096060	169719399	61245	SRX529137	SRS598834	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01165	0.00109	0.99622	0.72322	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Brain	Nervous System
38015	38015	SRR1265741	SRX529136	SRS598833	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Brain Replicate 2 sRNAseq	GSM1376624	source name:Female Brain\|gender:female\|tissue:Brain\|genetic background:Wild type Singapore strain	Female Brain Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Brain	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Brain\|genetic background:Wild type Singapore strain	GSM1376624	GSM1376624: Female Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376624		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376624	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZB011_GGCTAC_L007_R1.fastq.gz	fastq	197790903.0	3878253.0	GSM1376624 r1	0:51	A:39219508;C:48781853;G:60339090;T:49430999;N:19453	51		39219508	48781853	60339090	49430999	19453	SRX529136	SRS598833	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00227	0.00019	0.99835	0.67164	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Brain	Nervous System
38016	38016	SRR1265740	SRX529135	SRS598832	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Female Brain Replicate 1 sRNAseq	GSM1376623	source name:Female Brain\|gender:female\|tissue:Brain\|genetic background:Wild type Singapore strain	Female Brain Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Female Brain	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Brain\|genetic background:Wild type Singapore strain	GSM1376623	GSM1376623: Female Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376623		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376623	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZB010_TAGCTT_L007_R1.fastq.gz	fastq	127765710.0	2505210.0	GSM1376623 r1	0:51	A:24845648;C:31103830;G:38874684;T:32929436;N:12112	51		24845648	31103830	38874684	32929436	12112	SRX529135	SRS598832	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.02647	0.00307	0.99368	0.59472	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Brain	Nervous System
38017	38017	SRR1265739	SRX529134	SRS598831	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Brain Replicate 3 sRNAseq	GSM1376622	source name:Male Brain\|gender:male\|tissue:Brain\|genetic background:Wild type Singapore strain	Male Brain Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Brain	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Brain\|genetic background:Wild type Singapore strain	GSM1376622	GSM1376622: Male Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376622		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376622	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZB009_TTAGGC_L007_R1.fastq.gz	fastq	749856876.0	14703076.0	GSM1376622 r1	0:51	A:142133111;C:197021938;G:231006890;T:179625504;N:69433	51		142133111	197021938	231006890	179625504	69433	SRX529134	SRS598831	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00196	0.00026	0.99843	0.64615	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Brain	Nervous System
38018	38018	SRR1265738	SRX529133	SRS598830	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Brain Replicate 2 sRNAseq	GSM1376621	source name:Male Brain\|gender:male\|tissue:Brain\|genetic background:Wild type Singapore strain	Male Brain Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Brain	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Brain\|genetic background:Wild type Singapore strain	GSM1376621	GSM1376621: Male Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376621		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376621	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZB008_CGATGT_L007_R1.fastq.gz	fastq	394620558.0	7737658.0	GSM1376621 r1	0:51	A:68213140;C:110690478;G:127130285;T:88550429;N:36226	51		68213140	110690478	127130285	88550429	36226	SRX529133	SRS598830	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.06427	0.00768	0.98859	0.77971	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Brain	Nervous System
38019	38019	SRR1265737	SRX529132	SRS598829	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Brain Replicate 1 sRNAseq	GSM1376620	source name:Male Brain\|gender:male\|tissue:Brain\|genetic background:Wild type Singapore strain	Male Brain Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Brain	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Brain\|genetic background:Wild type Singapore strain	GSM1376620	GSM1376620: Male Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376620		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376620	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZB007_ATCACG_L007_R1.fastq.gz	fastq	329742489.0	6465539.0	GSM1376620 r1	0:51	A:60032454;C:91021987;G:104188224;T:74471433;N:28391	51		60032454	91021987	104188224	74471433	28391	SRX529132	SRS598829	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00994	0.00098	0.99738	0.77713	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Brain	Nervous System
38020	38020	SRR1265736	SRX529131	SRS598827	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Embryo Replicate 3 sRNAseq	GSM1376619	source name:Embryo\|tissue:Embryo\|genetic background:Wild type Singapore strain	Embryo Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Embryo	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Embryo\|genetic background:Wild type Singapore strain	GSM1376619	GSM1376619: Embryo Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376619		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376619	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZE006_CTTGTA_L008_R1.fastq.gz	fastq	1714180635.0	33611385.0	GSM1376619 r1	0:51	A:338559677;C:431494863;G:537012008;T:406904091;N:209996	51		338559677	431494863	537012008	406904091	209996	SRX529131	SRS598827	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.09044	0.01776	0.97782	0.77023	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38021	38021	SRR1265735	SRX529130	SRS598828	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Embryo Replicate 2 sRNAseq	GSM1376618	source name:Embryo\|tissue:Embryo\|genetic background:Wild type Singapore strain	Embryo Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Embryo	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Embryo\|genetic background:Wild type Singapore strain	GSM1376618	GSM1376618: Embryo Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376618		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376618	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZE005_GGCTAC_L008_R1.fastq.gz	fastq	736486002.0	14440902.0	GSM1376618 r1	0:51	A:145757737;C:194417932;G:231157927;T:165060763;N:91643	51		145757737	194417932	231157927	165060763	91643	SRX529130	SRS598828	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01133	0.00234	0.99515	0.73854	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38022	38022	SRR1265734	SRX529129	SRS598825	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Embryo Replicate 1 sRNAseq	GSM1376617	source name:Embryo\|tissue:Embryo\|genetic background:Wild type Singapore strain	Embryo Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Embryo	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	tissue:Embryo\|genetic background:Wild type Singapore strain	GSM1376617	GSM1376617: Embryo Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376617		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376617	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZE004_TAGCTT_L008_R1.fastq.gz	fastq	477426912.0	9361312.0	GSM1376617 r1	0:51	A:93534991;C:123428376;G:148877677;T:111524753;N:61115	51		93534991	123428376	148877677	111524753	61115	SRX529129	SRS598825	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.02061	0.00461	0.99379	0.8448	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38023	38023	SRR1265744	SRX529128	SRS598826	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.		pubmed:26574018		Male Gut Replicate 2 sRNAseq	GSM1376627	source name:Male Gut\|gender:male\|tissue:Gut\|genetic background:Wild type Singapore strain	Male Gut Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Male Gut	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Gut\|genetic background:Wild type Singapore strain	GSM1376627	GSM1376627: Male Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376627		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376627	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP041544	MZG008_ACAGTG_L007_R1.fastq.gz	fastq	541064457.0	10609107.0	GSM1376627 r1	0:51	A:104798947;C:136927266;G:166713427;T:132575036;N:49781	51		104798947	136927266	166713427	132575036	49781	SRX529128	SRS598826	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00679	0.00072	0.99655	0.72132	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gut	Digestive System
38042	38042	SRR1371226	SRX585640	SRS631986	SRP043064	PRJNA252044	Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq]	GSE58344	Transcriptome Analysis	In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases	parent bioproject:PRJNA252043	pubmed:26961822		RPL5 MO [miRNA]	GSM1408095	tissue:embryo\|genotype/variation:RPL5 morpholino knockdown\|developmental stage:48hpf	RPL5 MO [miRNA]	FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9	embryo	Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration.	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf	genotype/variation:RPL5 morpholino knockdown\|developmental stage:48hpf	GSM1408095	GSM1408095: RPL5 MO [miRNA]; Danio rerio; miRNA Seq	GSM1408095		1	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	GEO Accession:GSM1408095	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP043064	s_7_IDX19_1.fq	fastq	1093234725.0	13496725.0	GSM1408095 r1	0:81	A:263908052;C:257987133;G:278889068;T:292410262;N:40210	81		263908052	257987133	278889068	292410262	40210	SRX585640	SRS631986	SRA169796	GEO	Beijing Institute of Genomics	1	3e-05	0.0	0.99991	0.5	81	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-06-10	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38043	38043	SRR1371225	SRX585639	SRS631982	SRP043064	PRJNA252044	Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq]	GSE58344	Transcriptome Analysis	In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases	parent bioproject:PRJNA252043	pubmed:26961822		morpholino control [miRNA]	GSM1408094	tissue:embryo\|genotype/variation:control morpholino\|developmental stage:48hpf	morpholino control [miRNA]	FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9	embryo	Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration.	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf	genotype/variation:control morpholino\|developmental stage:48hpf	GSM1408094	GSM1408094: morpholino control [miRNA]; Danio rerio; miRNA Seq	GSM1408094		1	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	GEO Accession:GSM1408094	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP043064			308681847.0	3810887.0	GSM1408094 r1	0:81	A:63686404;C:75263287;G:80056961;T:89650625;N:24570	81		63686404	75263287	80056961	89650625	24570	SRX585639	SRS631982	SRA169796	GEO	Beijing Institute of Genomics	1	8e-05	2e-05	0.99991	0.42857	81	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-06-10	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38046	38046	SRR1427469	SRX612649	SRS643610	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		28d	GSM1417152	source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	28d	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417152	GSM1417152: 28d; Danio rerio; miRNA Seq	GSM1417152		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417152	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465	28d.fq	bam	694299184.0	32089203.0	GSM1417152 r1	0:21.64 1:0	A:174747494;C:132129648;G:193085254;T:194336788;N:0	21	0	174747494	132129648	193085254	194336788	0	SRX612649	SRS643610	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93434	0.05272	0.98831	0.56642	23	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38047	38047	SRR1427468	SRX612648	SRS643609	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		72h	GSM1417151	source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	72h	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417151	GSM1417151: 72h; Danio rerio; miRNA Seq	GSM1417151		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417151	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465	72h.fq	fastq	689263089.0	31419317.0	GSM1417151 r1	0:21.94 1:0	A:161567060;C:125003691;G:193763870;T:208928468;N:0	21	0	161567060	125003691	193763870	208928468	0	SRX612648	SRS643609	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.93237	0.03751	0.98774	0.51765	20	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38048	38048	SRR1427467	SRX612647	SRS643608	SRP043465	PRJNA253203	Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration	GSE58702	Transcriptome Analysis	Background: Adult zebrafish spontaneously regenerate their retinas post damage. Although a number of genes and signaling pathways involved in regeneration have been identified the extent of mechanisms regulating regeneration is unclear. Small non coding RNAs microRNAs miRNAs that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration we knocked down the expression of the miRNA processing enzyme Dicer in retinas prior to light induced damage. Dicer loss significantly reduced proliferation of Müller glia derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration we collected retinas at different stages of light damage and performed small RNA high throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration. Overall design: Identification of miRNAs before during and post completion of zebrafish retinal regeneration		pubmed:25220904		0h	GSM1417150	source name:Retina\|strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	0h	Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome. Bowtie Langmead et al. 2009 was used to map the resulting reads to miRNA hairpin sequences from miRbase www.miRbase.org Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands Genome build: Zv9 Supplementary files format and content: text files showing miRNA abundance; located on the series level	Retina		Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012		strain:albino alb / \|age:adult\|genotype:wildtype\|tissue:retina	GSM1417150	GSM1417150: 0h; Danio rerio; miRNA Seq	GSM1417150		1	Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15 30 nt small RNAs were size selected ligated to 3’ and 5’ end adapters and amplified by RT PCR to generate small RNA libraries as described Wei et al. 2012. Libraries were constructed following the protocol published by Wei et al. 2012	GEO Accession:GSM1417150	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP043465	0h.bam	fastq	3005859202.0	134278309.0	GSM1417150 r1	0:22.39	A:762111385;C:628084257;G:836553469;T:779110091;N:0	22		762111385	628084257	836553469	779110091	0	SRX612647	SRS643608	SRA171872	GEO	Biological Sciences, Vanderbilt University	1	0.94362	0.03903	0.99093	0.5848	22	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2014-06-20	Adult	Adult	Eye	Sensory System
38252	38252	SRR1593717	SRX718003	SRS713863	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948		Zeb fish Emb t 24h	GSM1517418	tissue:embryo\|genotype/variation:WT\|developmental stage:embryo 24h	Zeb fish Emb t 24h	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	embryo		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 24h	GSM1517418	GSM1517418: Zeb fish Emb t 24h; Danio rerio; miRNA Seq	GSM1517418		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517418	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP048545	Zeb_fish_Emb_t_24h_1.fastq.gz	fastq	2747798604.0	53878404.0	GSM1517418 r1	0:51	A:675086979;C:579211488;G:812576920;T:680856005;N:67212	51		675086979	579211488	812576920	680856005	67212	SRX718003	SRS713863	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38253	38253	SRR1593716	SRX718002	SRS713862	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948		Zeb fish Emb t 30m	GSM1517417	tissue:embryo\|genotype/variation:WT\|developmental stage:embryo 30m	Zeb fish Emb t 30m	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	embryo		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 30m	GSM1517417	GSM1517417: Zeb fish Emb t 30m; Danio rerio; miRNA Seq	GSM1517417		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517417	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP048545	Zeb_fish_Emb_t_30m_1.fastq.gz	fastq	3380715591.0	66288541.0	GSM1517417 r1	0:51	A:854040134;C:726173965;G:952338238;T:848081062;N:82192	51		854040134	726173965	952338238	848081062	82192	SRX718002	SRS713862	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	1e-05	0.0	0.99997	1.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38254	38254	SRR1593715	SRX718001	SRS713861	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948		Zeb fish Emb t 10m	GSM1517416	tissue:embryo\|genotype/variation:WT\|developmental stage:embryo 10m	Zeb fish Emb t 10m	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	embryo		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 10m	GSM1517416	GSM1517416: Zeb fish Emb t 10m; Danio rerio; miRNA Seq	GSM1517416		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517416	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP048545	Zeb_fish_Emb_t_10m_1.fastq.gz	fastq	3339395697.0	65478347.0	GSM1517416 r1	0:51	A:847877403;C:714050198;G:934084609;T:843302102;N:81385	51		847877403	714050198	934084609	843302102	81385	SRX718001	SRS713861	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38255	38255	SRR1593714	SRX718000	SRS713860	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948		Zeb fish Emb t 0m	GSM1517415	tissue:egg\|genotype/variation:WT\|developmental stage:embryo 0m	Zeb fish Emb t 0m	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	egg		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 0m	GSM1517415	GSM1517415: Zeb fish Emb t 0m; Danio rerio; miRNA Seq	GSM1517415		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517415	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP048545	Zeb_fish_Emb_t_0m_1.fastq.gz	fastq	3135589293.0	61482143.0	GSM1517415 r1	0:51	A:800912828;C:671516191;G:883139862;T:779944407;N:76005	51		800912828	671516191	883139862	779944407	76005	SRX718000	SRS713860	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38256	38256	SRR1596061	SRX719267	SRS715451	SRP048591	PRJNA262865	Identification and Characterization of MicroRNAs in Zebrafish Spermatozoa by Illumina Sequencing	GSE61984	Other	MicroRNAs miRNAs are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA rRNA snRNA snoRNA and miRNA. By mapping to the zebrafish genome we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families including zebrafish specific families such as mir 731 mir 724 mir 725 mir 729 and mir 2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Overall design: Examination of small RNA populations in zebrafish spermatozoa		pubmed:26418264		zebrafish sperm	GSM1517943	tissue:Zebrafish Spermatozoa\|cell type:Spermatozoa\|strain:AB wild type	zebrafish sperm	The sequencing data were analyzed as described previously by Xu et al 2014. The low quality reads were filtered to remove reads without xxx 3’ adaptor 5’ adaptor contaminant reads reads without xxx insert fragment reads containing polyA stretches and reads of less than 18 nt. Next the remaining sequences clean reads were mapped to the zebrafish genome using SOAP with a tolerance of one mismatch to analyze their distribution The sequences were aligned against known miRNA precursors and mature miRNAs deposited in the miRBase 20.0 to identify conserved miRNAs. The clean reads were compared against the sRNAs rRNAs tRNAs snRNAs snoRNA miRNA deposited in the GenBank and Rfam http://www.sanger.ac.uk/resources/databases/rfam.html databases to annotate the sRNA sequences. Because some sRNA tags might map to more than one category we used priority rules to ensure that every unique sRNA was mapped to only one annotation as follows: rRNA etc. GenBank >Rfam >known miRNA >repeat >exon >intron. Genome build: miRBase 20.0 Supplementary files format and content: zebrafish miRNA count.txt include RPKM values of each known miRNA in this sample	Zebrafish Spermatozoa		Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.		cell type:Spermatozoa\|strain:AB wild type	GSM1517943	GSM1517943: zebrafish sperm; Danio rerio; miRNA Seq	GSM1517943		1	Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.	GEO Accession:GSM1517943	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP048591	zebrafish-sperm5.fq.bz2	fastq	588000000.0	12000000.0	GSM1517943 r1	0:49	A:122673394;C:136175879;G:140377184;T:188702650;N:70893	49		122673394	136175879	140377184	188702650	70893	SRX719267	SRS715451	SRA188511	GEO	SUN YAT-SEN UNIVERSITY	1	2e-05	0.0	0.99997	1.0	49	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-10-02	Zygote	Embryo	Oocyte	Reproductive System
38321	38321	SRR1732707	SRX822003	SRS801698	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727		Emb MO Ct 48hpf	GSM1571860	source name:Embryos MO Ct 48hpf\|tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:48hpf	Emb MO Ct 48hpf	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:48hpf	GSM1571860	GSM1571860: Emb MO Ct 48hpf; Danio rerio; miRNA Seq	GSM1571860		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571860	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP051503	L.T.fq.gz	fastq	338322717.0	11175516.0	GSM1571860 r1	0:30.27 1:0	A:72708202;C:91561004;G:102921744;T:71122135;N:9632	30	0	72708202	91561004	102921744	71122135	9632	SRX822003	SRS801698	SRA221043	GEO	IIT, CNR	1	0.86712	0.22408	0.92725	0.50365	23	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38322	38322	SRR1732706	SRX822002	SRS801697	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727		Emb MO Tbx5a 48hpf	GSM1571859	source name:Embryos MO Tbx5a 48hpf\|tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:48hpf	Emb MO Tbx5a 48hpf	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:48hpf	GSM1571859	GSM1571859: Emb MO Tbx5a 48hpf; Danio rerio; miRNA Seq	GSM1571859		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571859	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP051503	I.T.fq.gz	fastq	262219132.0	10137926.0	GSM1571859 r1	0:25.87 1:0	A:60415193;C:62111082;G:75168882;T:64515539;N:8436	25	0	60415193	62111082	75168882	64515539	8436	SRX822002	SRS801697	SRA221043	GEO	IIT, CNR	1	0.52287	0.13984	0.8788	0.6354	30	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38323	38323	SRR1732705	SRX822001	SRS801696	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727		Emb MO Ct 24hpf rep2	GSM1571858	source name:Embryos MO Ct 24hpf replicate2\|tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	Emb MO Ct 24hpf rep2	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 24hpf replicate2	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	GSM1571858	GSM1571858: Emb MO Ct 24hpf rep2; Danio rerio; miRNA Seq	GSM1571858		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571858	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP051503	H.T.fq.gz	fastq	281909951.0	10806197.0	GSM1571858 r1	0:26.09 1:0	A:66055828;C:65184020;G:81768559;T:68892445;N:9099	26	0	66055828	65184020	81768559	68892445	9099	SRX822001	SRS801696	SRA221043	GEO	IIT, CNR	1	0.56084	0.23499	0.86819	0.64638	22	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38324	38324	SRR1732704	SRX822000	SRS801695	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727		Emb MO Ct 24hpf rep1	GSM1571857	source name:Embryos MO Ct 24hpf replicate1\|tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	Emb MO Ct 24hpf rep1	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 24hpf replicate1	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	GSM1571857	GSM1571857: Emb MO Ct 24hpf rep1; Danio rerio; miRNA Seq	GSM1571857		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571857	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP051503	G.T.fq.gz	fastq	541546124.0	19319535.0	GSM1571857 r1	0:28.03 1:0	A:126881333;C:133281439;G:163930613;T:117435553;N:17186	28	0	126881333	133281439	163930613	117435553	17186	SRX822000	SRS801695	SRA221043	GEO	IIT, CNR	1	0.53436	0.20796	0.9009	0.55394	34	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38325	38325	SRR1732703	SRX821999	SRS801694	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727		Emb MO Tbx5a 24hpf rep2	GSM1571856	source name:Embryos MO Tbx5a 24hpf replicate2\|tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	Emb MO Tbx5a 24hpf rep2	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 24hpf replicate2	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	GSM1571856	GSM1571856: Emb MO Tbx5a 24hpf rep2; Danio rerio; miRNA Seq	GSM1571856		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571856	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP051503	F.T.fq.gz	fastq	362513460.0	13684345.0	GSM1571856 r1	0:26.49 1:0	A:82709386;C:83987865;G:107681867;T:88122760;N:11582	26	0	82709386	83987865	107681867	88122760	11582	SRX821999	SRS801694	SRA221043	GEO	IIT, CNR	1	0.58925	0.2498	0.86821	0.65549	30	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38326	38326	SRR1732702	SRX821998	SRS801693	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727		Emb MO Tbx5a 24hpf rep1	GSM1571855	source name:Embryos MO Tbx5a 24hpf replicate1\|tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	Emb MO Tbx5a 24hpf rep1	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 24hpf replicate1	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	GSM1571855	GSM1571855: Emb MO Tbx5a 24hpf rep1; Danio rerio; miRNA Seq	GSM1571855		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571855	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP051503	E.T.fq.gz	fastq	399134579.0	13766109.0	GSM1571855 r1	0:28.99 1:0	A:88725326;C:102855219;G:121123717;T:86418155;N:12162	28	0	88725326	102855219	121123717	86418155	12162	SRX821998	SRS801693	SRA221043	GEO	IIT, CNR	1	0.66472	0.25948	0.89623	0.54913	34	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
39609	39609	SRR1873571	SRX915251	SRS870223	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		fins	GSM1630515	source name:adult fins 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:fins\|developmental stage:adult\|age:1 year	fins	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult fins 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:fins\|developmental stage:adult\|age:1 year	GSM1630515	GSM1630515: fins; Danio rerio; miRNA Seq	GSM1630515		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630515	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			113161.0	2108.0	GSM1630515 r1	0:4 1:49.68	A:30303;C:30710;G:27210;T:24785;N:153	4	49	30303	30710	27210	24785	153	SRX915251	SRS870223	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		50	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Fin	Surface Structure
39610	39610	SRR1873570	SRX915250	SRS870224	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		skin	GSM1630514	source name:adult skin 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:skin\|developmental stage:adult\|age:1 year	skin	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult skin 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:skin\|developmental stage:adult\|age:1 year	GSM1630514	GSM1630514: skin; Danio rerio; miRNA Seq	GSM1630514		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630514	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			79232.0	1527.0	GSM1630514 r1	0:4 1:47.89	A:20622;C:23508;G:19017;T:15967;N:118	4	47	20622	23508	19017	15967	118	SRX915250	SRS870224	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		53	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Skin	Surface Structure
39611	39611	SRR1873569	SRX915249	SRS870225	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		heart	GSM1630513	source name:adult heart 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:heart\|developmental stage:adult\|age:1 year	heart	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult heart 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:heart\|developmental stage:adult\|age:1 year	GSM1630513	GSM1630513: heart; Danio rerio; miRNA Seq	GSM1630513		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630513	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			39500.0	711.0	GSM1630513 r1	0:4 1:51.56	A:11300;C:9125;G:9195;T:9835;N:45	4	51	11300	9125	9195	9835	45	SRX915249	SRS870225	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		53	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Heart	Cardiovascular System
39612	39612	SRR1873568	SRX915248	SRS870226	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		gills	GSM1630512	source name:adult gills 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:gills\|developmental stage:adult\|age:1 year	gills	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult gills 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:gills\|developmental stage:adult\|age:1 year	GSM1630512	GSM1630512: gills; Danio rerio; miRNA Seq	GSM1630512		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630512	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			189248.0	3563.0	GSM1630512 r1	0:4 1:49.11	A:48212;C:55198;G:44765;T:40711;N:362	4	49	48212	55198	44765	40711	362	SRX915248	SRS870226	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		44	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Gill	Respiratory System
39613	39613	SRR1873567	SRX915247	SRS870227	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		eyes	GSM1630511	source name:adult eyes 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:eyes\|developmental stage:adult\|age:1 year	eyes	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult eyes 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:eyes\|developmental stage:adult\|age:1 year	GSM1630511	GSM1630511: eyes; Danio rerio; miRNA Seq	GSM1630511		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630511	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			173069.0	3135.0	GSM1630511 r1	0:4 1:51.21	A:50732;C:44705;G:40960;T:36324;N:348	4	51	50732	44705	40960	36324	348	SRX915247	SRS870227	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		52	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Eye	Sensory System
39614	39614	SRR1873566	SRX915246	SRS870228	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		brain	GSM1630510	source name:adult brain 1 year old\|strain/background:AB\|genotype/variation:wild type\|tissue:brain\|developmental stage:adult\|age:1 year	brain	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	adult brain 1 year old		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:brain\|developmental stage:adult\|age:1 year	GSM1630510	GSM1630510: brain; Danio rerio; miRNA Seq	GSM1630510		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630510	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			688279.0	12620.0	GSM1630510 r1	0:4 1:50.54	A:205782;C:180028;G:171745;T:129693;N:1031	4	50	205782	180028	171745	129693	1031	SRX915246	SRS870228	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		48	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Brain	Nervous System
39615	39615	SRR1873565	SRX915245	SRS870229	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		adult	GSM1630509	source name:entire adult\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:adult\|age:1 year	adult	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	entire adult		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:adult\|age:1 year	GSM1630509	GSM1630509: adult; Danio rerio; miRNA Seq	GSM1630509		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630509	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			361024.0	6498.0	GSM1630509 r1	0:4 1:51.56	A:104704;C:84406;G:83224;T:87843;N:847	4	51	104704	84406	83224	87843	847	SRX915245	SRS870229	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Adult	Adult	Trunk	Surface Structure
39616	39616	SRR1873564	SRX915244	SRS870230	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		45dpf	GSM1630508	source name:45 dpf embryos\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:45dpf	45dpf	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	45 dpf embryos		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:45dpf	GSM1630508	GSM1630508: 45dpf; Danio rerio; miRNA Seq	GSM1630508		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630508	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			123960.0	2248.0	GSM1630508 r1	0:4 1:51.14	A:38130;C:31332;G:30088;T:24223;N:187	4	51	38130	31332	30088	24223	187	SRX915244	SRS870230	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		52	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Juvenile	Juvenile	Trunk	Surface Structure
39617	39617	SRR1873563	SRX915243	SRS870231	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		5dpf	GSM1630507	source name:5 dpf embryos\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:5dpf	5dpf	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	5 dpf embryos		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:5dpf	GSM1630507	GSM1630507: 5dpf; Danio rerio; miRNA Seq	GSM1630507		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630507	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			168981.0	3060.0	GSM1630507 r1	0:4 1:51.22	A:51895;C:42870;G:40864;T:32741;N:611	4	51	51895	42870	40864	32741	611	SRX915243	SRS870231	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		50	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Larval	Larval	Trunk	Surface Structure
39618	39618	SRR1873562	SRX915242	SRS870232	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		96hpf	GSM1630506	source name:96 hpf embryos\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:96hpf	96hpf	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	96 hpf embryos		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:96hpf	GSM1630506	GSM1630506: 96hpf; Danio rerio; miRNA Seq	GSM1630506		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630506	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			61235.0	1109.0	GSM1630506 r1	0:4 1:51.22	A:18594;C:15084;G:15091;T:12247;N:219	4	51	18594	15084	15091	12247	219	SRX915242	SRS870232	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		52	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Larval	Larval	Trunk	Surface Structure
39619	39619	SRR1873561	SRX915241	SRS870233	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		72hpf	GSM1630505	source name:72 hpf embryos\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:72hpf	72hpf	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	72 hpf embryos		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:72hpf	GSM1630505	GSM1630505: 72hpf; Danio rerio; miRNA Seq	GSM1630505		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630505	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			778415.0	14183.0	GSM1630505 r1	0:4 1:50.88	A:231211;C:186354;G:190297;T:169348;N:1205	4	50	231211	186354	190297	169348	1205	SRX915241	SRS870233	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		48	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Larval	Larval	Trunk	Surface Structure
39620	39620	SRR1873560	SRX915240	SRS870234	SRP056014	PRJNA277780	Identification of small non coding RNAs in zebrafish	GSE66718	Transcriptome Analysis	MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.		pubmed:26694924		24hpf	GSM1630504	source name:24 hpf embryos\|strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:24hpf	24hpf	Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs…	24 hpf embryos		100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.	strain/background:AB\|genotype/variation:wild type\|tissue:whole body\|developmental stage:embryo\|age:24hpf	GSM1630504	GSM1630504: 24hpf; Danio rerio; miRNA Seq	GSM1630504		1	100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.	GEO Accession:GSM1630504	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	LS454	454 GS FLX		SRP056014			6831.0	129.0	GSM1630504 r1	0:4 1:48.95	A:1947;C:1747;G:1688;T:1424;N:25	4	48	1947	1747	1688	1424	25	SRX915240	SRS870234	SRA246117	GEO	University of Aveiro	1	0.0	0.0	1.0		46	T	under 1.2% mapping rate	legacy	early	3prime	size_fractionation	unknown	bulk	other_seq	454	Portugal	2015-03-09	Pharyngula	Embryo	Trunk	Surface Structure
39627	39627	SRR1931774	SRX970023	SRS885229	SRP056603	PRJNA279522	tRNA sequencing in Danio rerio	PRJNA279522	Other	Small RNA sequencing to look for disruption of CCA nucleotidyltransferase activity post TRNT1 knockdown.				WT Danio rerio	tRNAseq000 WT	breed:not collected\|age:5 day\|sex:not collected\|tissue:whole\|phenotype:normal morphology\|BioSampleModel:Model organism or animal									tRNA sequencing WT	tRNA sequencing WT	WT	1			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>	SRP056603	2-WT_S1_L001_R1_001.fastq.gz	fastq	1588656656.0	10577741.0	tRNA sequencing WT	0:150.19 1:0	A:478698865;C:376122807;G:338649726;T:395185202;N:56	150	0	478698865	376122807	338649726	395185202	56	SRX970023	SRS885229	SRA248889	University of Iowa\|Stephen A. Wynn Institute for Vision Research	University of Iowa	1	3e-05	0.0	0.99989	0.4	151	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2015-08-09	Larval	Larval	Undetermined	Undetermined
39628	39628	SRR1931761	SRX970012	SRS885221	SRP056603	PRJNA279522	tRNA sequencing in Danio rerio	PRJNA279522	Other	Small RNA sequencing to look for disruption of CCA nucleotidyltransferase activity post TRNT1 knockdown.				TRNT1 KD	tRNAseq000 MO	breed:not collected\|age:5 day\|sex:not collected\|tissue:whole\|phenotype:normal morphology\|BioSampleModel:Model organism or animal									tRNA sequencing of TRNT1 KD	tRNA sequencing of TRNT1 KD	1	1			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>	SRP056603	3-mutant1-TRNT-M0_S2_L001_R1_001.fastq.gz	fastq	1355519463.0	9025087.0	tRNA sequencing of TRNT1 KD	0:150.19 1:0	A:399052503;C:312898077;G:288848586;T:354720282;N:15	150	0	399052503	312898077	288848586	354720282	15	SRX970012	SRS885221	SRA248889	University of Iowa\|Stephen A. Wynn Institute for Vision Research	University of Iowa	1	0.00012	0.0	0.99965	0.78947	151	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2015-08-09	Larval	Larval	Undetermined	Undetermined
39703	39703	SRR2057604	SRX1054376	SRS957216	SRP059278	PRJNA286201	MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq]	GSE69690	Transcriptome Analysis	The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA286199	pubmed:26657204		Emb MO Ct 48hpf [miRNA seq]	GSM1707594	source name:Embryos MO Ct 48hpf\|strain background:AB\|infected with:MO C\|tissue:embryo\|developmental stage:48hpf	Emb MO Ct 48hpf [miRNA seq]	Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	strain background:AB\|infected with:MO C\|tissue:embryo\|developmental stage:48hpf	GSM1707594	GSM1707594: Emb MO Ct 48hpf [miRNA seq]; Danio rerio; miRNA Seq	GSM1707594		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1707594	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP059278	Dre_FC_4.fq.gz	fastq	1033068440.0	25826711.0	GSM1707594 r1	0:40	A:417902194;C:195580811;G:153264728;T:266159736;N:160971	40		417902194	195580811	153264728	266159736	160971	SRX1054376	SRS957216	SRA272222	GEO	IIT, CNR	1	0.05412	0.01319	0.97693	0.22489	40	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2015-06-09	Hatching	Embryo	Embryo Imprecise	All anatomical structures
39704	39704	SRR2057603	SRX1054375	SRS957217	SRP059278	PRJNA286201	MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq]	GSE69690	Transcriptome Analysis	The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA286199	pubmed:26657204		Emb MO Tbx5a 48hpf [miRNA seq]	GSM1707593	source name:Embryos MO Tbx5a 48hpf\|strain background:AB\|infected with:MO Tbx5a\|tissue:embryo\|developmental stage:48hpf	Emb MO Tbx5a 48hpf [miRNA seq]	Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	strain background:AB\|infected with:MO Tbx5a\|tissue:embryo\|developmental stage:48hpf	GSM1707593	GSM1707593: Emb MO Tbx5a 48hpf [miRNA seq]; Danio rerio; miRNA Seq	GSM1707593		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1707593	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP059278	Dre_FC_3.fq.gz	fastq	1038855840.0	25971396.0	GSM1707593 r1	0:40	A:430923990;C:193052690;G:149627446;T:265119627;N:132087	40		430923990	193052690	149627446	265119627	132087	SRX1054375	SRS957217	SRA272222	GEO	IIT, CNR	1	0.01858	0.00322	0.98699	0.23156	40	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2015-06-09	Hatching	Embryo	Embryo Imprecise	All anatomical structures
39760	39760	SRR2127901	SRX1118699	SRS1011434	SRP061587	PRJNA290964	Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos	GSE71346	Transcriptome Analysis	To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.		pubmed:30090366		6 48 0.5µM OTA [miRNA seq]	GSM1832841	tissue:embryo control\|strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:0.5 µM ochratoxin A from 6 hpf to 48 hpf	6 48 0.5µM OTA [miRNA seq]	Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome	embryo control	6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf.	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	zebrafish embryos were selected at 6 hph with normal development.	strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:0.5 µM ochratoxin A from 6 hpf to 48 hpf	GSM1832841	GSM1832841: 6 48 0.5µM OTA [miRNA seq]; Danio rerio; miRNA Seq	GSM1832841		1	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	GEO Accession:GSM1832841	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP061587	6_48_0.5um_OTA.fastq.gz	fastq	310077729.0	6130868.0	GSM1832841 r1	0:50.58 1:0	A:74462826;C:72958352;G:87201353;T:75455198;N:0	50	0	74462826	72958352	87201353	75455198	0	SRX1118699	SRS1011434	SRA280185	GEO	ntu	1	0.00671	0.00134	0.99594	0.39026	51	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Unknown	2015-07-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
39761	39761	SRR2127900	SRX1118698	SRS1011435	SRP061587	PRJNA290964	Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos	GSE71346	Transcriptome Analysis	To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.		pubmed:30090366		6 48 control [miRNA seq]	GSM1832840	tissue:embryo control\|strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:n1 control	6 48 control [miRNA seq]	Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome	embryo control	6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf.	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	zebrafish embryos were selected at 6 hph with normal development.	strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:n1 control	GSM1832840	GSM1832840: 6 48 control [miRNA seq]; Danio rerio; miRNA Seq	GSM1832840		1	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	GEO Accession:GSM1832840	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP061587	6_48_control.fastq.gz	fastq	308947811.0	6107500.0	GSM1832840 r1	0:50.58 1:0	A:75126425;C:71798677;G:85490341;T:76532368;N:0	50	0	75126425	71798677	85490341	76532368	0	SRX1118698	SRS1011435	SRA280185	GEO	ntu	1	0.00833	0.00166	0.99476	0.42762	51	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Unknown	2015-07-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
40972	40972	SRR3498294	SRX1756840	SRS1433371	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 72hpf E2	GSM2150819	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	NoEndo 72hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150819	GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq	GSM2150819		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150819	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	NoEndo_72hpf_E2.fastq.gz	fastq	797509876.0	10493551.0	GSM2150819 r1	0:76	A:182564842;C:199547592;G:199064466;T:216287390;N:45586	76		182564842	199547592	199064466	216287390	45586	SRX1756840	SRS1433371	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40973	40973	SRR3498293	SRX1756839	SRS1433370	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 72hpf E1	GSM2150818	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	NoEndo 72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150818	GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq	GSM2150818		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150818	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	NoEndo_72hpf_E1.fastq.gz	fastq	1864172232.0	24528582.0	GSM2150818 r1	0:76	A:426671762;C:469538477;G:458132395;T:509711525;N:118073	76		426671762	469538477	458132395	509711525	118073	SRX1756839	SRS1433370	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40974	40974	SRR3498292	SRX1756838	SRS1433369	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 6dpf E1	GSM2150817	source name:Endothelial cell\|developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	NoEndo 6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	GSM2150817	GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq	GSM2150817		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150817	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	NoEndo_6dpf_E1.fastq.gz	fastq	1414849364.0	18616439.0	GSM2150817 r1	0:76	A:315250036;C:366906308;G:364673112;T:367938758;N:81150	76		315250036	366906308	364673112	367938758	81150	SRX1756838	SRS1433369	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40975	40975	SRR3498291	SRX1756837	SRS1433368	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 48hpf E2	GSM2150816	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	NoEndo 48hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150816	GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq	GSM2150816		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150816	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	NoEndo_48hpf_E2.fastq.gz	fastq	553364740.0	7281115.0	GSM2150816 r1	0:76	A:129173344;C:134804122;G:141026546;T:148331467;N:29261	76		129173344	134804122	141026546	148331467	29261	SRX1756837	SRS1433368	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05	0.0	0.99997	0.0	76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40976	40976	SRR3498290	SRX1756836	SRS1433367	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 48hpf E1	GSM2150815	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	NoEndo 48hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150815	GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq	GSM2150815		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150815	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	NoEndo_48hpf_E1.fastq.gz	fastq	1204752152.0	15852002.0	GSM2150815 r1	0:76	A:297517299;C:293969730;G:317491224;T:295696492;N:77407	76		297517299	293969730	317491224	295696492	77407	SRX1756836	SRS1433367	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40977	40977	SRR3498289	SRX1756835	SRS1433366	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 24hpf E1	GSM2150814	source name:Endothelial cell\|developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	NoEndo 24hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	GSM2150814	GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq	GSM2150814		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150814	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	NoEndo_24hpf_E1.fastq.gz	fastq	1422085704.0	18711654.0	GSM2150814 r1	0:76	A:347700492;C:356065333;G:376424133;T:341806001;N:89745	76		347700492	356065333	376424133	341806001	89745	SRX1756835	SRS1433366	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Pharyngula	Embryo	Endothelium	Cardiovascular System
40978	40978	SRR3498288	SRX1756834	SRS1433365	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 72hpf E2	GSM2150813	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	Endo 72hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150813	GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq	GSM2150813		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150813	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	Endo_72hpf_E2.fastq.gz	fastq	438128980.0	5764855.0	GSM2150813 r1	0:76	A:101851745;C:114159902;G:115733669;T:106360221;N:23443	76		101851745	114159902	115733669	106360221	23443	SRX1756834	SRS1433365	SRA424808	GEO	Internal Medicine, Yale University	1	2e-05	1e-05	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40979	40979	SRR3498287	SRX1756833	SRS1433364	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 72hpf E1	GSM2150812	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	Endo 72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150812	GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq	GSM2150812		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150812	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	Endo_72hpf_E1.fastq.gz	fastq	1267915068.0	16683093.0	GSM2150812 r1	0:76	A:321606522;C:310505837;G:323829249;T:311892892;N:80568	76		321606522	310505837	323829249	311892892	80568	SRX1756833	SRS1433364	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40980	40980	SRR3498286	SRX1756832	SRS1433363	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 6dpf E1	GSM2150811	source name:Endothelial cell\|developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	Endo 6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	GSM2150811	GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq	GSM2150811		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150811	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	Endo_6dpf_E1.fastq.gz	fastq	890474824.0	11716774.0	GSM2150811 r1	0:76	A:230419087;C:212029155;G:232306960;T:215672618;N:47004	76		230419087	212029155	232306960	215672618	47004	SRX1756832	SRS1433363	SRA424808	GEO	Internal Medicine, Yale University	1	2e-05	1e-05	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40981	40981	SRR3498285	SRX1756831	SRS1433362	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 48hpf E2	GSM2150810	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	Endo 48hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150810	GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq	GSM2150810		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150810	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	Endo_48hpf_E2.fastq.gz	fastq	1254556624.0	16507324.0	GSM2150810 r1	0:76	A:316229540;C:323340793;G:307552357;T:307354555;N:79379	76		316229540	323340793	307552357	307354555	79379	SRX1756831	SRS1433362	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40982	40982	SRR3498284	SRX1756830	SRS1433361	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 48hpf E1	GSM2150809	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	Endo 48hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150809	GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq	GSM2150809		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150809	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	Endo_48hpf_E1.fastq.gz	fastq	1449497080.0	19072330.0	GSM2150809 r1	0:76	A:362564557;C:370330864;G:364749441;T:351760774;N:91444	76		362564557	370330864	364749441	351760774	91444	SRX1756830	SRS1433361	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40983	40983	SRR3498283	SRX1756829	SRS1433360	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 24hpf E1	GSM2150808	source name:Endothelial cell\|developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	Endo 24hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	GSM2150808	GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq	GSM2150808		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150808	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer		SRP074848	Endo_24hpf_E1.fastq.gz	fastq	1527500440.0	20098690.0	GSM2150808 r1	0:76	A:356712587;C:354608109;G:432977038;T:383106520;N:96186	76		356712587	354608109	432977038	383106520	96186	SRX1756829	SRS1433360	SRA424808	GEO	Internal Medicine, Yale University	1	0.0	0.0	1.0		76	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Pharyngula	Embryo	Endothelium	Cardiovascular System
41244	41244	SRR3953261	SRX1977497	SRS1585138	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		500 μg/l BDE47 treatment miRNA	GSM2252184	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	500 μg/l BDE47 treatment miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252184	GSM2252184: 500 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq	GSM2252184		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252184	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896	Sample_500_1_filtered.fastq.gz	fastq	427211416.0	18037304.0	GSM2252184 r1	0:23.68 1:0	A:104654735;C:95575450;G:107353019;T:119612667;N:15545	23	0	104654735	95575450	107353019	119612667	15545	SRX1977497	SRS1585138	SRA444471	GEO	Tongji University	1	0.85356	0.06282	0.88609	0.63407	21	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41245	41245	SRR3953260	SRX1977496	SRS1585141	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		5 μg/l BDE47 treatment miRNA	GSM2252183	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	5 μg/l BDE47 treatment miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252183	GSM2252183: 5 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq	GSM2252183		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252183	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896	Sample_5_1_filtered.fastq.gz	fastq	450698842.0	19202408.0	GSM2252183 r1	0:23.47 1:0	A:112159775;C:101086362;G:111723361;T:125713845;N:15499	23	0	112159775	101086362	111723361	125713845	15499	SRX1977496	SRS1585141	SRA444471	GEO	Tongji University	1	0.84838	0.06014	0.88637	0.6441	23	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41246	41246	SRR3953259	SRX1977495	SRS1585136	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		s DMSO vehicle miRNA	GSM2252182	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	s DMSO vehicle miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252182	GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq	GSM2252182		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252182	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896	Sample_s_1_filtered.fq.gz	fastq	383701320.0	16988819.0	GSM2252182 r1	0:22.59 1:0	A:97700155;C:85144858;G:93319367;T:107531046;N:5894	22	0	97700155	85144858	93319367	107531046	5894	SRX1977495	SRS1585136	SRA444471	GEO	Tongji University	1	0.86023	0.05501	0.89534	0.59715	22	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41247	41247	SRR3953258	SRX1977494	SRS1585137	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		c Wildtype miRNA	GSM2252181	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	c Wildtype miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252181	GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq	GSM2252181		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252181	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896	Sample_c_1_filtered.fastq.gz	fastq	413922462.0	17365113.0	GSM2252181 r1	0:23.84 1:0	A:102173642;C:93233248;G:103684592;T:114815345;N:15635	23	0	102173642	93233248	103684592	114815345	15635	SRX1977494	SRS1585137	SRA444471	GEO	Tongji University	1	0.85083	0.06831	0.88152	0.63274	27	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
43050	43050	SRR5883565	SRX3049654	SRS2396336	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver BPA 4 6	GSM2722577	tissue:Liver\|exposure:100 nM BPA	Liver BPA 4 6	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:100 nM BPA	GSM2722577	GSM2722577: Liver BPA 4 6; Danio rerio; miRNA Seq	GSM2722577		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722577	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397	12_GGTAGC_LALL_R1_001.fastq.gz	fastq	461508486.0	9049186.0	GSM2722577 r1	0:51	A:92718489;C:120118265;G:143926288;T:103539215;N:1206229	51		92718489	120118265	143926288	103539215	1206229	SRX3049654	SRS2396336	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.02792	0.00247	0.99602	0.60254	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
43051	43051	SRR5883564	SRX3049653	SRS2396335	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver BPA 1 3	GSM2722576	tissue:Liver\|exposure:100 nM BPA	Liver BPA 1 3	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:100 nM BPA	GSM2722576	GSM2722576: Liver BPA 1 3; Danio rerio; miRNA Seq	GSM2722576		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722576	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397	11_GAGTGG_LALL_R1_001.fastq.gz	fastq	587697684.0	11523484.0	GSM2722576 r1	0:51	A:131489823;C:140167421;G:171253226;T:143217998;N:1569216	51		131489823	140167421	171253226	143217998	1569216	SRX3049653	SRS2396335	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.03603	0.00774	0.98492	0.65361	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
43052	43052	SRR5883563	SRX3049652	SRS2396334	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver CNTRL 4 5	GSM2722575	tissue:Liver\|exposure:Control	Liver CNTRL 4 5	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:Control	GSM2722575	GSM2722575: Liver CNTRL 4 5; Danio rerio; miRNA Seq	GSM2722575		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722575	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397	10_CGTACG_LALL_R1_001.fastq.gz	fastq	407289621.0	7986071.0	GSM2722575 r1	0:51	A:84982391;C:104532595;G:122785928;T:93918201;N:1070506	51		84982391	104532595	122785928	93918201	1070506	SRX3049652	SRS2396334	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.13902	0.01445	0.99086	0.57915	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
43053	43053	SRR5883562	SRX3049651	SRS2396333	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver CNTRL 1 3	GSM2722574	tissue:Liver\|exposure:Control	Liver CNTRL 1 3	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:Control	GSM2722574	GSM2722574: Liver CNTRL 1 3; Danio rerio; miRNA Seq	GSM2722574		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722574	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397	9_GTTTCG_LALL_R1_001.fastq.gz	fastq	379997073.0	7450923.0	GSM2722574 r1	0:51	A:79538003;C:96525448;G:113901755;T:89020494;N:1011373	51		79538003	96525448	113901755	89020494	1011373	SRX3049651	SRS2396333	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.00447	0.0005	0.99626	0.57217	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System
44999	44999	SRR6411468	SRX3504483	SRS2782037	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Gut 4 miRNA	GSM2898188	source name:Gut\|tissue:Gut\|Sex:male	Gut 4 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Gut	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Gut\|Sex:male	GSM2898188	GSM2898188: Gut 4 miRNA; Danio rerio; miRNA Seq	GSM2898188		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898188	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389	4.fastq.gz	fastq	643103727.0	12609877.0	GSM2898188 r1	0:51	A:158299708;C:154230134;G:180978224;T:147874496;N:1721165	51		158299708	154230134	180978224	147874496	1721165	SRX3504483	SRS2782037	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.0075	0.00106	0.99671	0.56044	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Gut	Digestive System
45000	45000	SRR6411467	SRX3504482	SRS2782036	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Gut 3 miRNA	GSM2898187	source name:Gut\|tissue:Gut\|Sex:male	Gut 3 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Gut	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Gut\|Sex:male	GSM2898187	GSM2898187: Gut 3 miRNA; Danio rerio; miRNA Seq	GSM2898187		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898187	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389	3.fastq.gz	fastq	657326148.0	12888748.0	GSM2898187 r1	0:51	A:155617794;C:161709285;G:186002579;T:152250836;N:1745654	51		155617794	161709285	186002579	152250836	1745654	SRX3504482	SRS2782036	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.11293	0.00924	0.99399	0.58458	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Gut	Digestive System
45001	45001	SRR6411466	SRX3504481	SRS2782035	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Liver 2 miRNA	GSM2898186	source name:Liver\|tissue:Liver\|Sex:male	Liver 2 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Liver\|Sex:male	GSM2898186	GSM2898186: Liver 2 miRNA; Danio rerio; miRNA Seq	GSM2898186		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898186	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389	2.fastq.gz	fastq	407289621.0	7986071.0	GSM2898186 r1	0:51	A:84982391;C:104532595;G:122785928;T:93918201;N:1070506	51		84982391	104532595	122785928	93918201	1070506	SRX3504481	SRS2782035	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.13902	0.01444	0.99076	0.58988	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Liver	Liver and Biliary System
45002	45002	SRR6411465	SRX3504480	SRS2782034	SRP127389	PRJNA427282	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA]	GSE108436	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis.	parent bioproject:PRJNA427275	pubmed:30386173		Liver 1 miRNA	GSM2898185	source name:Liver\|tissue:Liver\|Sex:male	Liver 1 miRNA	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		tissue:Liver\|Sex:male	GSM2898185	GSM2898185: Liver 1 miRNA; Danio rerio; miRNA Seq	GSM2898185		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2898185	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127389	1.fastq.gz	fastq	379997073.0	7450923.0	GSM2898185 r1	0:51	A:79538003;C:96525448;G:113901755;T:89020494;N:1011373	51		79538003	96525448	113901755	89020494	1011373	SRX3504480	SRS2782034	SRA641250	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.00448	0.00052	0.99632	0.58707	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2017-12-22	Undetermined	Adult	Liver	Liver and Biliary System
49101	49101	SRR7726444	SRX4582847	SRS3697100	SRP158508	PRJNA487021	MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish	GSE118850	Transcriptome Analysis	Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos gata5/6 morphants and control embryos. Overall design: The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo.				G56 miRNA	GSM3349122	tissue:G56 embryos\|genotype:gata4/5/6 knockdown\|developmental stage:embryos\|age:14hpf	G56 miRNA	The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single read sequencing recipe. Fastx fastx toolkit 0.0.13.2 was used to preprocess the original reads of the sequence. The CLC genomics workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database version 19.0. Genome build: Sanger miRBase database version 19.0 Supplementary files format and content: .csv file includes small RNA sequences and counts Supplementary files format and content: .xls file includes effective reads and fold changes	G56 embryos	Morpholinos MOs were purchased from Gene Tools http://www.gene tools.com. MOs were dissolved in nanopure water and microinjected into the embryos at xxx cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6.	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The 3’ and 5’ adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	Zebrafish were housed in the zebrafish room of Model Animal Research Center Nanjing University in accordance with IACUC approved protocol. All methods were performed in accordance with the relevant guidelines and regulations.	genotype:gata4/5/6 knockdown\|developmental stage:embryos\|age:14hpf	GSM3349122	GSM3349122: G56 miRNA; Danio rerio; miRNA Seq	GSM3349122		1	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The three prime and five prime adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	GEO Accession:GSM3349122	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina MiSeq		SRP158508			655037050.0	13100741.0	GSM3349122 r1	0:50 1:0	A:161448247;C:135821164;G:200213833;T:156824030;N:729776	50	0	161448247	135821164	200213833	156824030	729776	SRX4582847	SRS3697100	SRA761361	GEO	Nanjing University	1	0.00066	6e-05	0.99896	0.64583	50	T	under 1.2% mapping rate	illumina	miseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-08-21	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
49102	49102	SRR7726443	SRX4582846	SRS3697099	SRP158508	PRJNA487021	MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish	GSE118850	Transcriptome Analysis	Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos gata5/6 morphants and control embryos. Overall design: The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo.				WT miRNA	GSM3349121	tissue:WT embryos\|genotype:wild type\|developmental stage:embryos\|age:14hpf	WT miRNA	The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single read sequencing recipe. Fastx fastx toolkit 0.0.13.2 was used to preprocess the original reads of the sequence. The CLC genomics workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database version 19.0. Genome build: Sanger miRBase database version 19.0 Supplementary files format and content: .csv file includes small RNA sequences and counts Supplementary files format and content: .xls file includes effective reads and fold changes	WT embryos	Morpholinos MOs were purchased from Gene Tools http://www.gene tools.com. MOs were dissolved in nanopure water and microinjected into the embryos at xxx cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6.	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The 3’ and 5’ adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	Zebrafish were housed in the zebrafish room of Model Animal Research Center Nanjing University in accordance with IACUC approved protocol. All methods were performed in accordance with the relevant guidelines and regulations.	genotype:wild type\|developmental stage:embryos\|age:14hpf	GSM3349121	GSM3349121: WT miRNA; Danio rerio; miRNA Seq	GSM3349121		1	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The three prime and five prime adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	GEO Accession:GSM3349121	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina MiSeq		SRP158508			627151350.0	12543027.0	GSM3349121 r1	0:50 1:0	A:153340174;C:128104541;G:192611227;T:152395340;N:700068	50	0	153340174	128104541	192611227	152395340	700068	SRX4582846	SRS3697099	SRA761361	GEO	Nanjing University	1	0.0006	0.00012	0.99904	0.60759	50	T	under 1.2% mapping rate	illumina	miseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-08-21	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
49778	49778	SRR8040485	SRX4870997	SRS3925977	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914			t32lps7 miRNA seq	GSM3427264	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps7 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427264	GSM3427264: t32lps7 miRNA seq; Danio rerio; miRNA Seq	GSM3427264		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427264	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			2979410976.0	39202776.0	GSM3427264 r1	0:76 1:0	A:680890914;C:823795284;G:813206458;T:661494032;N:24288	76	0	680890914	823795284	813206458	661494032	24288	SRX4870997	SRS3925977	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00172	0.00036	0.99659	0.5774	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49779	49779	SRR8040484	SRX4870996	SRS3925976	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914			t32lps5 miRNA seq	GSM3427263	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps5 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427263	GSM3427263: t32lps5 miRNA seq; Danio rerio; miRNA Seq	GSM3427263		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427263	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			3748512888.0	49322538.0	GSM3427263 r1	0:76 1:0	A:827904249;C:957754082;G:980630416;T:982193588;N:30553	76	0	827904249	957754082	980630416	982193588	30553	SRX4870996	SRS3925976	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00336	0.00087	0.99657	0.58597	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49780	49780	SRR8040483	SRX4870995	SRS3925975	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914			t32lps3 miRNA seq	GSM3427262	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps3 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427262	GSM3427262: t32lps3 miRNA seq; Danio rerio; miRNA Seq	GSM3427262		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427262	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			738838712.0	9721562.0	GSM3427262 r1	0:76 1:0	A:153616530;C:205779426;G:206416216;T:173020629;N:5911	76	0	153616530	205779426	206416216	173020629	5911	SRX4870995	SRS3925975	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01547	0.00084	0.99614	0.65654	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49781	49781	SRR8040482	SRX4870994	SRS3925974	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914			t32lps2 miRNA seq	GSM3427261	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps2 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427261	GSM3427261: t32lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427261		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427261	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			826032068.0	10868843.0	GSM3427261 r1	0:76 1:0	A:173874245;C:231864336;G:237091534;T:183195515;N:6438	76	0	173874245	231864336	237091534	183195515	6438	SRX4870994	SRS3925974	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00642	0.00032	0.99799	0.64507	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic 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");;