metadata: run_metadata: 12 rows where devstage_curation = "Pharyngula" and experiment.library

12 rows where devstage_curation = "Pharyngula" 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.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.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
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
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
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
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
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
41406	41406	SRR4423130	SRX2245314	SRS1745863	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 10 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:prim 16 stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: prim 16 stage31 hpf	348 10	348 10	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S10small.fastq	fastq	427409571.0	5026564.0	S10small.fastq	0:85.03	A:98026046;C:116630773;G:114413502;T:98339250;N:0	85		98026046	116630773	114413502	98339250	0	SRX2245314	SRS1745863	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.81583	0.17938	0.9094	0.63072	126	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
41407	41407	SRR4423129	SRX2245313	SRS1745862	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 9 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:prim 5 stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: prim 5 stage24 hpf	348 9	348 9	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S09small.fastq	fastq	516614705.0	6246071.0	S09small.fastq	0:82.71	A:117786535;C:140799134;G:139362428;T:118666608;N:0	82		117786535	140799134	139362428	118666608	0	SRX2245313	SRS1745862	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.81132	0.18952	0.88925	0.69719	17	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
60887	60887	SRR12628234	SRX9110497	SRS7353480	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs		pubmed:33506864	h24 2: PGCs 24hpf repeat2	GSM4777194	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h24 2: PGCs 24hpf repeat2	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777194	GSM4777194: h24 2: PGCs 24hpf repeat2; Danio rerio; miRNA Seq	GSM4777194		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777194	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h24_2.fastq	fastq	4024398750.0	26829325.0	GSM4777194 r1	0:150 1:0	A:1030703487;C:1025857271;G:1004392553;T:963376583;N:68856	150	0	1030703487	1025857271	1004392553	963376583	68856	SRX9110497	SRS7353480	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00025	0.0	0.99997	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Pharyngula	Embryo	Gonad	Reproductive System
60888	60888	SRR12628233	SRX9110496	SRS7353479	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs		pubmed:33506864	h24 1: PGCs 24hpf repeat1	GSM4777193	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h24 1: PGCs 24hpf repeat1	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777193	GSM4777193: h24 1: PGCs 24hpf repeat1; Danio rerio; miRNA Seq	GSM4777193		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777193	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h24_1.fastq	fastq	2223111450.0	14820743.0	GSM4777193 r1	0:150 1:0	A:510125618;C:561938103;G:577742482;T:573267493;N:37754	150	0	510125618	561938103	577742482	573267493	37754	SRX9110496	SRS7353479	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.0004	0.0	0.99993	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Pharyngula	Embryo	Gonad	Reproductive 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");;