RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

31 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Embryo Imprecise"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.platform 2

tissue_curation_coarse 1

tissue_curation 1

  • Embryo Imprecise · 31 ✖

technology 1

experiment.library_strategy 1

  • RNA-Seq · 31 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 31 ✖

experiment.library_layout 1

devstage_curation_coarse 1

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.centername 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.title run.attributes 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.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
15081 15081 ERR12476478 ERX11852299 ERS17743543 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242D Starved 1242SD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:201 277053 1242SD 1     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SD_S14_L003_R1_001.fastq.gz fastq 95457398.0 1268859.0 ena RUN TAB 15 01 2024 21:42:36:202 277054 0:75.23 A:33339157;C:18598733;G:20350072;T:23148005;N:21431 75       33339157 18598733 20350072 23148005 21431 ERX11852299 ERS17743543 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown size_fractionation unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
36195 36195 SRR042434 SRX020028 SRS066219 SRP002411 PRJNA126003 A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity GSE21503 Transcriptome Analysis Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf   pubmed:20448148   MZago2 mutant YΔ90 GSM540646   tissue:48hpf embryo MZago2 mutant|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 Δ90/Δ90 MZago2 mutant YΔ90 Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. 48hpf embryo MZago2 mutant   Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 Δ90/Δ90 GSM540646 GSM540646: MZago2 mutant YΔ90 GSM540646: MZago2 mutant YΔ90 GSM540646: MZago2 mutant YΔ90 1   GEO Accession:GSM540646 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP002411     Ago2_ydelta90.fastq fastq 437752008.0 12159778.0 GSM540646 1 0:36 A:96750665;C:83495585;G:119239752;T:138073795;N:192211 36       96750665 83495585 119239752 138073795 192211 SRX020028 SRS066219 SRA012683 GEO Giraldez Lab, Genetics, Yale University 1 0.03964   0.0   0.99985   0.00052   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2010-05-04 Hatching Embryo Embryo Imprecise All anatomical structures
36196 36196 SRR042433 SRX020027 SRS066218 SRP002411 PRJNA126003 A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity GSE21503 Transcriptome Analysis Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf   pubmed:20448148   WT2 GSM540645   tissue:48hpf embryo WT|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type WT2 Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. 48hpf embryo WT   Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type GSM540645 GSM540645: WT2 GSM540645: WT2 GSM540645: WT2 1   GEO Accession:GSM540645 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP002411     WT2.fastq fastq 59530030.0 1700858.0 GSM540645 1 0:35 A:12981942;C:11521313;G:16378279;T:18609524;N:38972 35       12981942 11521313 16378279 18609524 38972 SRX020027 SRS066218 SRA012683 GEO Giraldez Lab, Genetics, Yale University 1 0.06435   0.0   0.99995   0.0   35   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2010-05-04 Hatching Embryo Embryo Imprecise All anatomical structures
36197 36197 SRR042432 SRX020026 SRS066217 SRP002411 PRJNA126003 A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity GSE21503 Transcriptome Analysis Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf   pubmed:20448148   MZdicer mutant2 hu896 GSM540644   tissue:48hpf embryo Mzdicer mutant|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896 MZdicer mutant2 hu896 Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. 48hpf embryo Mzdicer mutant   Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896 GSM540644 GSM540644: MZdicer mutant2 hu896 GSM540644: MZdicer mutant2 hu896 GSM540644: MZdicer mutant2 hu896 1   GEO Accession:GSM540644 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP002411     MZdicer2_hu896.fastq fastq 4268740.0 121964.0 GSM540644 1 0:35 A:813936;C:1034356;G:1131604;T:1280756;N:8088 35       813936 1034356 1131604 1280756 8088 SRX020026 SRS066217 SRA012683 GEO Giraldez Lab, Genetics, Yale University 1 0.03836   0.0009   0.99849   0.3021   35   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2010-05-04 Hatching Embryo Embryo Imprecise All anatomical structures
36198 36198 SRR042431 SRX020025 SRS066216 SRP002411 PRJNA126003 A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity GSE21503 Transcriptome Analysis Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf   pubmed:20448148   WT1 GSM540643   tissue:48hpf embryo WT|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type WT1 Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. 48hpf embryo WT   Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type GSM540643 GSM540643: WT1 GSM540643: WT1 GSM540643: WT1 1   GEO Accession:GSM540643 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP002411   quality book char:@|quality scoring system:log odds WT1.fastq fastq 26959392.0 748872.0 GSM540643 1 0:36 A:6097309;C:6093948;G:6950185;T:7813829;N:4121 36       6097309 6093948 6950185 7813829 4121 SRX020025 SRS066216 SRA012683 GEO Giraldez Lab, Genetics, Yale University 1 0.0022   0.0   0.99993   0.0   36   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2010-05-04 Hatching Embryo Embryo Imprecise All anatomical structures
36199 36199 SRR042430 SRX020024 SRS066215 SRP002411 PRJNA126003 A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity GSE21503 Transcriptome Analysis Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf   pubmed:20448148   MZdicer mutant1 hu715 GSM540642   tissue:48hpf embryo Mzdicer mutant|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715 MZdicer mutant1 hu715 Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. 48hpf embryo Mzdicer mutant   Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715 GSM540642 GSM540642: MZdicer mutant1 hu715 GSM540642: MZdicer mutant1 hu715 GSM540642: MZdicer mutant1 hu715 1   GEO Accession:GSM540642 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP002411   quality book char:@|quality scoring system:log odds MZdicer1_hu715.fastq fastq 11972772.0 332577.0 GSM540642 1 0:36 A:2703131;C:3062840;G:3338413;T:2867600;N:788 36       2703131 3062840 3338413 2867600 788 SRX020024 SRS066215 SRA012683 GEO Giraldez Lab, Genetics, Yale University 1 0.00678   0.00073   0.99847   0.3421   36   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2010-05-04 Hatching Embryo Embryo Imprecise All anatomical structures
36333 36333 SRR398324 SRX115582 SRS285699 SRP010291 PRJNA150927 miR 221 is required for endothelial tip cell behaviors during vascular development GSE35078 Transcriptome Analysis Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.   pubmed:22340502   kdrl:egfp min microRNA GSM861786   tissue:FACS isolated egfp negative cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:non endothelial cells kdrl:egfp min microRNA The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. FACS isolated egfp negative cells Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers.   genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:non endothelial cells GSM861786 GSM861786: kdrl:egfp min microRNA; Danio rerio; RNA Seq GSM861786 1 GSM861786: kdrl:egfp min microRNA 1   GEO Accession:GSM861786 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> SRP010291     miRNA_GFP_MINUS.fastq.gz fastq 206441460.0 5734485.0 GSM861786 r1 0:36 A:53061964;C:48186825;G:47161433;T:53484016;N:4547222 36       53061964 48186825 47161433 53484016 4547222 SRX115582 SRS285699 SRA049243 GEO Nathan Lawson Lab, PGFE, Umass Medical School 1 0.01499   0.01416   0.99922   0.4   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2012-01-12 Pharyngula Embryo Embryo Imprecise All anatomical structures
36334 36334 SRR398323 SRX115581 SRS285698 SRP010291 PRJNA150927 miR 221 is required for endothelial tip cell behaviors during vascular development GSE35078 Transcriptome Analysis Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.   pubmed:22340502   kdrl:egfp pos microRNA GSM861785   tissue:FACS isolated kdrl:egfp positive cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:endothelial cells kdrl:egfp pos microRNA The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. FACS isolated kdrl:egfp positive cells Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers.   genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:endothelial cells GSM861785 GSM861785: kdrl:egfp pos microRNA; Danio rerio; RNA Seq GSM861785 1 GSM861785: kdrl:egfp pos microRNA 1   GEO Accession:GSM861785 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> SRP010291     miRNA_GFP_PLUS.fastq.gz fastq 265629096.0 7378586.0 GSM861785 r1 0:36 A:67563811;C:62134550;G:62283750;T:67966396;N:5680589 36       67563811 62134550 62283750 67966396 5680589 SRX115581 SRS285698 SRA049243 GEO Nathan Lawson Lab, PGFE, Umass Medical School 1 0.01356   0.01279   0.99924   0.3125   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2012-01-12 Pharyngula Embryo Embryo Imprecise All anatomical structures
36482 36482 SRR530894 SRX172598 SRS352620 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   60hpf TCDD 3 GSM979608   source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD 60hpf TCDD 3 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD GSM979608 GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq GSM979608 1 GSM979608: 60hpf TCDD 3 1   GEO Accession:GSM979608 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646         1007239870.0 28778282.0 GSM979608 r1 0:35 0:284531587;1:248579138;2:213782485;3:258771962;.:1574698 35                 SRX172598 SRS352620 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.04824   0.03   0.981   0.49967   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Hatching Embryo Embryo Imprecise All anatomical structures
36483 36483 SRR530893 SRX172597 SRS352619 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   60hpf TCDD 2 GSM979607   source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD 60hpf TCDD 2 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD GSM979607 GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq GSM979607 1 GSM979607: 60hpf TCDD 2 1   GEO Accession:GSM979607 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0011.csfasta SOLiD_native 407347325.0 11638495.0 GSM979607 r1 0:35 0:99062820;1:113921998;2:81336108;3:112422342;.:604057 35                 SRX172597 SRS352619 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.04258   0.02455   0.98287   0.5048   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Hatching Embryo Embryo Imprecise All anatomical structures
36484 36484 SRR530892 SRX172596 SRS352618 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   60hpf TCDD 1 GSM979606   source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD 60hpf TCDD 1 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD GSM979606 GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq GSM979606 1 GSM979606: 60hpf TCDD 1 1   GEO Accession:GSM979606 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0010.csfasta SOLiD_native 680837045.0 19452487.0 GSM979606 r1 0:35 0:165079839;1:167219862;2:147812329;3:199659766;.:1065249 35                 SRX172596 SRS352618 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.02295   0.01479   0.98884   0.55191   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Hatching Embryo Embryo Imprecise All anatomical structures
36485 36485 SRR530891 SRX172595 SRS352617 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   60hpf DMSO 3 GSM979605   source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO 60hpf DMSO 3 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO GSM979605 GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq GSM979605 1 GSM979605: 60hpf DMSO 3 1   GEO Accession:GSM979605 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0009.csfasta SOLiD_native 495019840.0 14143424.0 GSM979605 r1 0:35 0:134854583;1:126192934;2:102458221;3:130747961;.:766141 35                 SRX172595 SRS352617 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.06707   0.04409   0.97285   0.5058   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Hatching Embryo Embryo Imprecise All anatomical structures
36486 36486 SRR530890 SRX172594 SRS352616 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   60hpf DMSO 2 GSM979604   source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO 60hpf DMSO 2 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO GSM979604 GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq GSM979604 1 GSM979604: 60hpf DMSO 2 1   GEO Accession:GSM979604 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0008.qual SOLiD_native 440403425.0 12582955.0 GSM979604 r1 0:35 0:110302240;1:106481197;2:104551283;3:118415637;.:653068 35                 SRX172594 SRS352616 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.05778   0.03522   0.97423   0.50884   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Hatching Embryo Embryo Imprecise All anatomical structures
36487 36487 SRR530889 SRX172593 SRS352615 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   60hpf DMSO 1 GSM979603   source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO 60hpf DMSO 1 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO GSM979603 GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq GSM979603 1 GSM979603: 60hpf DMSO 1 1   GEO Accession:GSM979603 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0007.csfasta MH_0007.qual SOLiD_native SOLiD_native 583800490.0 16680014.0 GSM979603 r1 0:35 0:166122108;1:149534173;2:111986455;3:155255262;.:902492 35                 SRX172593 SRS352615 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.05644   0.03829   0.9781   0.4997   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Hatching Embryo Embryo Imprecise All anatomical structures
36488 36488 SRR530888 SRX172592 SRS352614 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   36hpf TCDD 3 GSM979602   source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD 36hpf TCDD 3 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD GSM979602 GSM979602: 36hpf TCDD 3; Danio rerio; RNA Seq GSM979602 1 GSM979602: 36hpf TCDD 3 1   GEO Accession:GSM979602 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0006.qual MH_0006.csfasta SOLiD_native SOLiD_native 214059615.0 6115989.0 GSM979602 r1 0:35 0:56635752;1:54053300;2:48355842;3:54677354;.:337367 35                 SRX172592 SRS352614 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.13044   0.07694   0.95704   0.53005   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
36489 36489 SRR530887 SRX172591 SRS352613 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   36hpf TCDD 2 GSM979601   source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD 36hpf TCDD 2 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD GSM979601 GSM979601: 36hpf TCDD 2; Danio rerio; RNA Seq GSM979601 1 GSM979601: 36hpf TCDD 2 1   GEO Accession:GSM979601 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646         388475115.0 11099289.0 GSM979601 r1 0:35 0:103611863;1:99408831;2:86592980;3:98238344;.:623097 35                 SRX172591 SRS352613 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.15634   0.10763   0.96069   0.47755   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
36490 36490 SRR530886 SRX172590 SRS352612 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   36hpf TCDD 1 GSM979600   source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD 36hpf TCDD 1 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD GSM979600 GSM979600: 36hpf TCDD 1; Danio rerio; RNA Seq GSM979600 1 GSM979600: 36hpf TCDD 1 1   GEO Accession:GSM979600 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0004.csfasta SOLiD_native 366389765.0 10468279.0 GSM979600 r1 0:35 0:100797199;1:91391785;2:80412155;3:93217840;.:570786 35                 SRX172590 SRS352612 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.14106   0.09874   0.95724   0.49685   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
36491 36491 SRR530885 SRX172589 SRS352611 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   36hpf DMSO 3 GSM979599   source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO 36hpf DMSO 3 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO GSM979599 GSM979599: 36hpf DMSO 3; Danio rerio; RNA Seq GSM979599 1 GSM979599: 36hpf DMSO 3 1   GEO Accession:GSM979599 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0003.csfasta SOLiD_native 2108864835.0 60253281.0 GSM979599 r1 0:35 0:591489585;1:461028640;2:379338654;3:673048278;.:3959678 35                 SRX172589 SRS352611 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.09321   0.06563   0.98244   0.50577   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
36492 36492 SRR530884 SRX172588 SRS352610 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   36hpf DMSO 2 GSM979598   source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO 36hpf DMSO 2 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO GSM979598 GSM979598: 36hpf DMSO 2; Danio rerio; RNA Seq GSM979598 1 GSM979598: 36hpf DMSO 2 1   GEO Accession:GSM979598 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0002.qual SOLiD_native 363765885.0 10393311.0 GSM979598 r1 0:35 0:99316622;1:92947128;2:80099367;3:90839592;.:563176 35                 SRX172588 SRS352610 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.13435   0.09839   0.96146   0.49914   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
36493 36493 SRR530883 SRX172587 SRS352609 SRP014646 PRJNA171751 MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] GSE39808 Transcriptome Analysis Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing parent bioproject:PRJNA171747 pubmed:22921993   36hpf DMSO 1 GSM979597   source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO 36hpf DMSO 1 CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files Embryos   Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.   strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO GSM979597 GSM979597: 36hpf DMSO 1; Danio rerio; RNA Seq GSM979597 1 GSM979597: 36hpf DMSO 1 1   GEO Accession:GSM979597 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> SRP014646     MH_0001F3.csfasta MH_0001F3_QV.qual SOLiD_native SOLiD_native 309659000.0 8847400.0 GSM979597 r1 0:35 0:83729307;1:78100521;2:70827559;3:76531823;.:469790 35                 SRX172587 SRS352609 SRA056525 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.56398   0.33182   0.91092   0.5842   35   B   usable mapping rate legacy early unknown size_fractionation unknown bulk unknown unknown   United States 2012-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
37121 37121 SRR952244 SRX334986 SRS469877 SRP028754 PRJNA214896 Danio rerio Transcriptome or Gene expression PRJNA214896 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     embryonic development General Sample for zebrafish 1 cell   breed:wild type zebrafish                 1 cell developmental stage of zebrafish 1 cell 1 Zebrafish embryos were collected at 1 cell 0.2 hpf 16 cell 1.5 hpf 512 cell 2.75 hpf oblong 3.7 hpf 5.3 hpf 50% epibody 6 somite 12 hpf 24 hpf day1 hpf and 48 hpf day2 stages. Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</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> SRP028754     s1-cell.fq fastq 1002077048.0 20450552.0 1 cell 0:49 1:0 A:210178307;C:226566574;G:255003953;T:310259058;N:69156 49 0     210178307 226566574 255003953 310259058 69156 SRX334986 SRS469877 SRA097312 Huazhong University of Science and Technology|CUCKOO Huazhong University of Science and Technology 1 0.0001   3e-05   0.99977   0.58333   49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2014-08-12 Multi-stage Embryo Embryo Imprecise All anatomical structures
37122 37122 SRR953569 SRX336211 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 48hpf of zebrafish development 48hpf stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     day2.fq fastq 628342631.0 12823319.0 48hpf 0:49 A:148145336;C:136573491;G:166351863;T:177234943;N:36998 49       148145336 136573491 166351863 177234943 36998 SRX336211 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 1e-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 2015-07-22 Hatching Embryo Embryo Imprecise All anatomical structures
37123 37123 SRR953568 SRX336209 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 24hpf of zebrafish development 24hpf stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     day1.fq fastq 575258726.0 11739974.0 24hpf 0:49 A:132961290;C:123570971;G:152269421;T:166422672;N:34372 49       132961290 123570971 152269421 166422672 34372 SRX336209 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 0.0   0.0   1.0       49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2015-07-22 Pharyngula Embryo Embryo Imprecise All anatomical structures
37124 37124 SRR953567 SRX336208 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 6 somite of zebrafish development 6 somite stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     s6-somite.fq fastq 1023786106.0 20893594.0 6 somite 0:49 A:231966134;C:225595480;G:271618141;T:294536757;N:69594 49       231966134 225595480 271618141 294536757 69594 SRX336208 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 0.0   0.0   1.0       49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2015-07-22 Segmentation Embryo Embryo Imprecise All anatomical structures
37125 37125 SRR953532 SRX336173 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 5.3hpf of zebrafish development 5.3hpf stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     s53-h.fq fastq 1007880412.0 20568988.0 5.3hpf 0:49 A:226128850;C:222011747;G:262126135;T:297544238;N:69442 49       226128850 222011747 262126135 297544238 69442 SRX336173 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 0.0   0.0   1.0       49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2015-07-22 Gastrula Embryo Embryo Imprecise All anatomical structures
37126 37126 SRR953531 SRX336172 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 oblong of zebrafish development oblong stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     oblong.fq fastq 1016928850.0 20753650.0 oblong 0:49 A:224798674;C:224915257;G:271761873;T:295384794;N:68252 49       224798674 224915257 271761873 295384794 68252 SRX336172 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 1e-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 2015-07-22 Blastula Embryo Embryo Imprecise All anatomical structures
37127 37127 SRR953530 SRX336171 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 512 cell of zebrafish development 512 cell stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     s512-cell.fq fastq 991550035.0 20235715.0 512 cell 0:49 A:213493042;C:219665976;G:263488396;T:294834622;N:67999 49       213493042 219665976 263488396 294834622 67999 SRX336171 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 4e-05   1e-05   0.99993   1.0   49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2015-07-22 Blastula Embryo Embryo Imprecise All anatomical structures
37128 37128 SRR953522 SRX336167 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 16 cell of zebrafish development 16 cell stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862     s16-cell.fq fastq 857702468.0 17504132.0 16 cell stage 0:49 A:188518867;C:188172489;G:222316155;T:258636924;N:58033 49       188518867 188172489 222316155 258636924 58033 SRX336167 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 3e-05   1e-05   0.99993   1.0   49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2015-07-22 Cleavage Embryo Embryo Imprecise All anatomical structures
37129 37129 SRR953087 SRX335692 SRS470740 SRP028862 PRJNA215266 Danio rerio Transcriptome or Gene expression PRJNA215266 Other During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.     small RNA sequencing for zebrafish early development General Sample for zebrafish zebrafish early development   breed:wild type zebrafish                 1 cell of zebrafish development 1 cell stage 1 Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.     RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> SRP028862         1002077048.0 20450552.0 1 cell stage 0:49 A:210178307;C:226566574;G:255003953;T:310259058;N:69156 49       210178307 226566574 255003953 310259058 69156 SRX335692 SRS470740 SRA098041 Huazhong University of Science and Technology|cuckoo Huazhong University of Science and Technology 1 0.0001   3e-05   0.99975   0.76923   49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
37905 37905 SRR1138230 SRX445323 SRS540474 SRP035565 PRJNA236050 Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq GSE54259 Transcriptome Analysis In this study we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique several deregulated genes and miRNAs were found to be related with hematopoiesis vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs with partial verification from previous studies revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases parent bioproject:PRJNA236073 pubmed:25189322;pubmed:26961822   RPS24 MO miRNA Seq GSM1311219   tissue:embryo|genotype:RPS24 morpholino knockdown|developmental stage:embryo 48hpf RPS24 MO miRNA Seq 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:RPS24 morpholino knockdown|developmental stage:embryo 48hpf GSM1311219 GSM1311219: RPS24 MO miRNA Seq; Danio rerio; RNA Seq GSM1311219   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:GSM1311219 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP035565     s_7_IDX18_1.fq fastq 883114731.0 10902651.0 GSM1311219 r1 0:81 A:189355667;C:238092214;G:225845644;T:229789867;N:31339 81       189355667 238092214 225845644 229789867 31339 SRX445323 SRS540474 SRA128456 GEO Beijing Institute of Genomics 1 4e-05   0.0   0.99991   1.0   81   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2014-01-21 Hatching Embryo Embryo Imprecise All anatomical structures
37906 37906 SRR1138229 SRX445322 SRS540473 SRP035565 PRJNA236050 Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq GSE54259 Transcriptome Analysis In this study we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique several deregulated genes and miRNAs were found to be related with hematopoiesis vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs with partial verification from previous studies revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases parent bioproject:PRJNA236073 pubmed:25189322;pubmed:26961822   morpholino control miRNA Seq GSM1311218   tissue:embryo|genotype:control morpholino|developmental stage:embryo 48hpf morpholino control miRNA Seq 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:control morpholino|developmental stage:embryo 48hpf GSM1311218 GSM1311218: morpholino control miRNA Seq; Danio rerio; RNA Seq GSM1311218   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:GSM1311218 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP035565     s_8_IDX21_1.fq fastq 308681847.0 3810887.0 GSM1311218 r1 0:81 A:63686404;C:75263287;G:80056961;T:89650625;N:24570 81       63686404 75263287 80056961 89650625 24570 SRX445322 SRS540473 SRA128456 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 2014-01-21 Hatching Embryo Embryo Imprecise All anatomical structures

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;