run_metadata
164 rows where experiment.library_selection = "size fractionation" and experiment.library_strategy = "RNA-Seq"
This data as json, CSV (advanced)
| 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 |
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| 10403 | 10403 | ERR8527374 | ERX8137561 | ERS10539829 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF2 | SAMEA12941033 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF2 p | ZF2 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:ren knockout | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF2_S2_L002_I1_001.fastq.gz ZF2_S2_L002_R1_001.fastq.gz ZF2_S2_L002_R2_001.fastq.gz | fastq fastq fastq | 38557081640.0 | 125185330.0 | E MTAB 11079 2:ZF2 S2 L002 | 0:8 1:150 2:150 | A:13781315856;C:6436030786;G:6578059630;T:10759631611;N:561117 | 8 | 150 | 150 | 13781315856 | 6436030786 | 6578059630 | 10759631611 | 561117 | ERX8137561 | ERS10539829 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.84449 | 0.0 | 0.09657 | 1.0 | 0.8242 | 0.52635 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 10404 | 10404 | ERR8527377 | ERX8137561 | ERS10539829 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF2 | SAMEA12941033 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF2 p | ZF2 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:ren knockout | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF2_S2_L001_I1_001.fastq.gz ZF2_S2_L001_R1_001.fastq.gz ZF2_S2_L001_R2_001.fastq.gz | fastq fastq fastq | 38872269128.0 | 126208666.0 | E MTAB 11079 2:ZF2 S2 L001 | 0:8 1:150 2:150 | A:15151865400;C:6355030057;G:6591732598;T:9763441371;N:530374 | 8 | 150 | 150 | 15151865400 | 6355030057 | 6591732598 | 9763441371 | 530374 | ERX8137561 | ERS10539829 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.84526 | 0.0 | 0.09779 | 1.0 | 0.82609 | 0.54388 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 10405 | 10405 | ERR8527376 | ERX8137560 | ERS10539828 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF1 | SAMEA12941032 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF1 p | ZF1 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:wild type | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF1_S1_L002_I1_001.fastq.gz ZF1_S1_L002_R1_001.fastq.gz ZF1_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 39415722500.0 | 127973125.0 | E MTAB 11079 2:ZF1 S1 L002 | 0:8 1:150 2:150 | A:14261012964;C:6339158428;G:6467430919;T:11323758989;N:576200 | 8 | 150 | 150 | 14261012964 | 6339158428 | 6467430919 | 11323758989 | 576200 | ERX8137560 | ERS10539828 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.81065 | 0.0 | 0.08289 | 1.0 | 0.82434 | 0.52903 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 10406 | 10406 | ERR8527375 | ERX8137560 | ERS10539828 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF1 | SAMEA12941032 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF1 p | ZF1 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:wild type | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF1_S1_L001_I1_001.fastq.gz ZF1_S1_L001_R1_001.fastq.gz ZF1_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 39744721324.0 | 129041303.0 | E MTAB 11079 2:ZF1 S1 L001 | 0:8 1:150 2:150 | A:15670316830;C:6278039908;G:6505806971;T:10257683184;N:544007 | 8 | 150 | 150 | 15670316830 | 6278039908 | 6505806971 | 10257683184 | 544007 | ERX8137560 | ERS10539828 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.81031 | 0.0 | 0.08495 | 1.0 | 0.82169 | 0.51724 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 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 | |||||||||||||||||||||||||||||
| 28490 | 28490 | SRR26319601 | SRX22027740 | SRS19100857 | SRP465070 | PRJNA1025141 | Danio rerio Raw sequence reads | PRJNA1025141 | Other | Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep. | Treatment | CX3 for transcriptome 3 | CX3 | strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.67 E|treatment:Treatment Group|BioSampleModel:Model organism or animal | ALST3 for transcriptome 3 | CX3 for transcriptome 3 | CX3 for transcriptome 3 | CX3 for transcriptome 3 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Ten | SRP465070 | Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz | fastq fastq | 6255596356.0 | 20929531.0 | Unknown AY803 03T0006 good 1.fq.gz | 0:149.44 1:149.44 | A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506 | 149 | 149 | 1657365560 | 1463722268 | 1467057724 | 1667269298 | 181506 | SRX22027740 | SRS19100857 | SRA1727563 | Soochow University|School of biology & basic medical sciences | Soochow University | 2 | 0.89228 | 0.91654 | 0.09286 | 0.09714 | 0.6588 | 0.65604 | 0.4631 | 0.45773 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2023-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||
| 28491 | 28491 | SRR26319602 | SRX22027739 | SRS19100854 | SRP465070 | PRJNA1025141 | Danio rerio Raw sequence reads | PRJNA1025141 | Other | Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep. | Treatment | CX2 for transcriptome 2 | CX2 | strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.66 E|treatment:Treatment Group|BioSampleModel:Model organism or animal | ALST2 for transcriptome 2 | CX2 for transcriptome 2 | CX2 for transcriptome 2 | CX2 for transcriptome 2 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Ten | SRP465070 | Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz | fastq fastq | 6598066464.0 | 22061446.0 | Unknown AY803 03T0005 good 1.fq.gz | 0:149.54 1:149.54 | A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217 | 149 | 149 | 1747291499 | 1543289262 | 1549193118 | 1758088368 | 204217 | SRX22027739 | SRS19100854 | SRA1727563 | Soochow University|School of biology & basic medical sciences | Soochow University | 2 | 0.88949 | 0.92148 | 0.08893 | 0.0947 | 0.65596 | 0.65228 | 0.46045 | 0.47087 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2023-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||
| 28492 | 28492 | SRR26319603 | SRX22027738 | SRS19100853 | SRP465070 | PRJNA1025141 | Danio rerio Raw sequence reads | PRJNA1025141 | Other | Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep. | Treatment | CX1 for transcriptome 1 | CX1 | strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.65 E|treatment:Treatment Group|BioSampleModel:Model organism or animal | ALST1 for transcriptome 1 | CX1 for transcriptome 1 | CX1 for transcriptome 1 | CX1 for transcriptome 1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Ten | SRP465070 | Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz | fastq fastq | 6478923586.0 | 21662443.0 | Unknown AY803 03T0004 good 1.fq.gz | 0:149.54 1:149.54 | A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990 | 149 | 149 | 1712718473 | 1518937459 | 1523570227 | 1723510437 | 186990 | SRX22027738 | SRS19100853 | SRA1727563 | Soochow University|School of biology & basic medical sciences | Soochow University | 2 | 0.89423 | 0.9176 | 0.08944 | 0.09254 | 0.6575 | 0.65458 | 0.4693 | 0.46842 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2023-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||
| 28493 | 28493 | SRR26319604 | SRX22027737 | SRS19100856 | SRP465070 | PRJNA1025141 | Danio rerio Raw sequence reads | PRJNA1025141 | Other | Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep. | Control | con3 for transcriptome 3 | con3 | strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.64 E|treatment:Control Group|BioSampleModel:Model organism or animal | con3 for transcriptome 3 | con3 for transcriptome 3 | con3 for transcriptome 3 | con3 for transcriptome 3 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Ten | SRP465070 | Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz | fastq fastq | 6341537566.0 | 21218597.0 | Unknown AY803 03T0003 good 1.fq.gz | 0:149.43 1:149.43 | A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250 | 149 | 149 | 1679811754 | 1483631833 | 1489430825 | 1688482904 | 180250 | SRX22027737 | SRS19100856 | SRA1727563 | Soochow University|School of biology & basic medical sciences | Soochow University | 2 | 0.88245 | 0.91856 | 0.09069 | 0.09654 | 0.66253 | 0.65817 | 0.46245 | 0.46336 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2023-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||
| 28494 | 28494 | SRR26319605 | SRX22027736 | SRS19100855 | SRP465070 | PRJNA1025141 | Danio rerio Raw sequence reads | PRJNA1025141 | Other | Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep. | Control | con2 for transcriptome 2 | con2 | strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.63 E|treatment:Control Group|BioSampleModel:Model organism or animal | con2 for transcriptome 2 | con2 for transcriptome 2 | con2 for transcriptome 2 | con2 for transcriptome 2 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Ten | SRP465070 | Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz | fastq fastq | 5709771178.0 | 19100144.0 | Unknown AY803 03T0002 good 1.fq.gz | 0:149.47 1:149.47 | A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283 | 149 | 149 | 1505730979 | 1342843084 | 1346105868 | 1514941964 | 149283 | SRX22027736 | SRS19100855 | SRA1727563 | Soochow University|School of biology & basic medical sciences | Soochow University | 2 | 0.8924 | 0.91903 | 0.09155 | 0.09604 | 0.65902 | 0.65593 | 0.4634 | 0.46028 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2023-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||
| 28495 | 28495 | SRR26319606 | SRX22027735 | SRS19100852 | SRP465070 | PRJNA1025141 | Danio rerio Raw sequence reads | PRJNA1025141 | Other | Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep. | Control | con1 for transcriptome 1 | con1 | strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.62 E|treatment:Control Group|BioSampleModel:Model organism or animal | con1 for transcriptome 1 | con1 for transcriptome 1 | con1 for transcriptome 1 | con1 for transcriptome 1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Ten | SRP465070 | Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz | fastq fastq | 6544586118.0 | 21872265.0 | Unknown AY803 03T0001 good 1.fq.gz | 0:149.61 1:149.61 | A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334 | 149 | 149 | 1731179229 | 1528367346 | 1541103688 | 1743735521 | 200334 | SRX22027735 | SRS19100852 | SRA1727563 | Soochow University|School of biology & basic medical sciences | Soochow University | 2 | 0.87588 | 0.92739 | 0.08683 | 0.09494 | 0.65711 | 0.6504 | 0.46774 | 0.47072 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2023-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||
| 31514 | 31514 | SRR28435337 | SRX24039257 | SRS20832031 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | cry dash / group 2 at CT 16 | Cryd CT16G2 | Unknown BA023 04T0008.fq.gz | isolate:The second group of cry dash / fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0008.fq.gz | Unknown BA023 04T0008.fq.gz | CT16 cry dash group2 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0008_good_2.fq.gz Unknown_BA023-04T0008_good_1.fq.gz | fastq fastq | 6928082472.0 | 23162452.0 | Unknown BA023 04T0008 good 1.fq.gz | 0:149.55 1:149.55 | A:1783381005;C:1671764458;G:1686432861;T:1786331460;N:172688 | 149 | 149 | 1783381005 | 1671764458 | 1686432861 | 1786331460 | 172688 | SRX24039257 | SRS20832031 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.96107 | 0.96048 | 0.06638 | 0.06578 | 0.68546 | 0.68582 | 0.46626 | 0.45803 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31515 | 31515 | SRR28435338 | SRX24039256 | SRS20832030 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | cry dash / group 1 at CT 16 | Cryd CT16G1 | Unknown BA023 04T0007.fq.gz | isolate:The first group of cry dash / fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0007.fq.gz | Unknown BA023 04T0007.fq.gz | CT16 cry dash group1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0007_good_2.fq.gz Unknown_BA023-04T0007_good_1.fq.gz | fastq fastq | 7247045982.0 | 24239568.0 | Unknown BA023 04T0007 good 1.fq.gz | 0:149.49 1:149.49 | A:1868252704;C:1747715656;G:1761213537;T:1869681292;N:182793 | 149 | 149 | 1868252704 | 1747715656 | 1761213537 | 1869681292 | 182793 | SRX24039256 | SRS20832030 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.95954 | 0.95937 | 0.0624 | 0.06218 | 0.68809 | 0.68765 | 0.47347 | 0.47429 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31516 | 31516 | SRR28435339 | SRX24039255 | SRS20832029 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | cry dash / group 2 at CT 4 | Cryd CT4G2 | Unknown BA023 04T0006.fq.gz | isolate:The second group of cry dash / fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0006.fq.gz | Unknown BA023 04T0006.fq.gz | CT4 cry dash group2 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0006_good_1.fq.gz Unknown_BA023-04T0006_good_2.fq.gz | fastq fastq | 7467294282.0 | 24985127.0 | Unknown BA023 04T0006 good 1.fq.gz | 0:149.43 1:149.43 | A:1940430660;C:1790773066;G:1798765445;T:1937139187;N:185924 | 149 | 149 | 1940430660 | 1790773066 | 1798765445 | 1937139187 | 185924 | SRX24039255 | SRS20832029 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.95702 | 0.95753 | 0.08848 | 0.08877 | 0.6829 | 0.68199 | 0.49417 | 0.49443 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31517 | 31517 | SRR28435340 | SRX24039254 | SRS20832028 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | cry dash / group 1 at CT 4 | Cryd CT4G1 | Unknown BA023 04T0005.fq.gz | isolate:The first group of cry dash / fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0005.fq.gz | Unknown BA023 04T0005.fq.gz | CT4 cry dash group1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0005_good_1.fq.gz Unknown_BA023-04T0005_good_2.fq.gz | fastq fastq | 6766310740.0 | 22646274.0 | Unknown BA023 04T0005 good 1.fq.gz | 0:149.39 1:149.39 | A:1762324132;C:1615995203;G:1625767974;T:1762055354;N:168077 | 149 | 149 | 1762324132 | 1615995203 | 1625767974 | 1762055354 | 168077 | SRX24039254 | SRS20832028 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.95588 | 0.95587 | 0.06663 | 0.06633 | 0.67911 | 0.67888 | 0.46701 | 0.47626 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31518 | 31518 | SRR28435341 | SRX24039253 | SRS20832027 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | WT group 2 at CT 16 | WT CT16G2 | Unknown BA023 04T0004.fq.gz | isolate:The second group of WT fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0004.fq.gz | Unknown BA023 04T0004.fq.gz | CT6 WT group2 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0004_good_2.fq.gz Unknown_BA023-04T0004_good_1.fq.gz | fastq fastq | 6830283170.0 | 22847843.0 | Unknown BA023 04T0004 good 1.fq.gz | 0:149.47 1:149.47 | A:1791839697;C:1618554485;G:1627518993;T:1792199298;N:170697 | 149 | 149 | 1791839697 | 1618554485 | 1627518993 | 1792199298 | 170697 | SRX24039253 | SRS20832027 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.9515 | 0.94997 | 0.08493 | 0.08422 | 0.67178 | 0.67316 | 0.47915 | 0.48187 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31519 | 31519 | SRR28435342 | SRX24039252 | SRS20832026 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | WT group 1 at CT 16 | WT CT16G1 | Unknown BA023 04T0003.fq.gz | isolate:The first group of WT fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0003.fq.gz | Unknown BA023 04T0003.fq.gz | CT6 WT group1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0003_good_1.fq.gz Unknown_BA023-04T0003_good_2.fq.gz | fastq fastq | 6430546584.0 | 21512133.0 | Unknown BA023 04T0003 good 1.fq.gz | 0:149.46 1:149.46 | A:1678015842;C:1530296350;G:1541505212;T:1680568743;N:160437 | 149 | 149 | 1678015842 | 1530296350 | 1541505212 | 1680568743 | 160437 | SRX24039252 | SRS20832026 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.94974 | 0.95051 | 0.08145 | 0.0819 | 0.6775 | 0.67848 | 0.47999 | 0.47986 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31520 | 31520 | SRR28435343 | SRX24039251 | SRS20832025 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | WT group 2 at CT 4 | WT CT4G2 | Unknown BA023 04T0002.fq.gz | isolate:The second group of WT fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0002.fq.gz | Unknown BA023 04T0002.fq.gz | CT4 WT group2 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0002_good_1.fq.gz Unknown_BA023-04T0002_good_2.fq.gz | fastq fastq | 7084078326.0 | 23701315.0 | Unknown BA023 04T0002 good 1.fq.gz | 0:149.44 1:149.44 | A:1855453089;C:1679520129;G:1688607029;T:1860319577;N:178502 | 149 | 149 | 1855453089 | 1679520129 | 1688607029 | 1860319577 | 178502 | SRX24039251 | SRS20832025 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.95393 | 0.95431 | 0.07799 | 0.07802 | 0.66728 | 0.66835 | 0.46237 | 0.47322 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 31521 | 31521 | SRR28435344 | SRX24039250 | SRS20832024 | SRP497569 | PRJNA1090643 | Danio rerio Raw sequence reads | PRJNA1090643 | Other | The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16. | WT group 1 at CT 4 | WT CT4G1 | Unknown BA023 04T0001.fq.gz | isolate:The first group of WT fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: larvae | Unknown BA023 04T0001.fq.gz | Unknown BA023 04T0001.fq.gz | CT4 WT group1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | HiSeq X Five | SRP497569 | Unknown_BA023-04T0001_good_2.fq.gz Unknown_BA023-04T0001_good_1.fq.gz | fastq fastq | 7360015710.0 | 24625447.0 | Unknown BA023 04T0001 good 1.fq.gz | 0:149.44 1:149.44 | A:1931324589;C:1743134275;G:1748699685;T:1936672740;N:184421 | 149 | 149 | 1931324589 | 1743134275 | 1748699685 | 1936672740 | 184421 | SRX24039250 | SRS20832024 | SRA1832685 | Soochow University|School of Biology & Basic Medical Sciences | Soochow University | 2 | 0.954 | 0.95301 | 0.08257 | 0.08182 | 0.66772 | 0.66906 | 0.47505 | 0.47577 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Unknown | 2024-03-25 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||
| 32923 | 32923 | SRR29498567 | SRX25008885 | SRS21709104 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | F2g | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F2g|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 10 | 10 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | F2g_R2.fq.gz F2g_R1.fq.gz | fastq fastq | 9101949000.0 | 30339830.0 | F2g R1.fq.gz | 0:150 1:150 | A:2052853923;C:2394247721;G:2773304460;T:1881440199;N:102697 | 150 | 150 | 2052853923 | 2394247721 | 2773304460 | 1881440199 | 102697 | SRX25008885 | SRS21709104 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.65449 | 0.37434 | 0.04313 | 0.12258 | 0.99519 | 0.99527 | 0.61425 | 0.56139 | 150 | 150 | B | B | mate2-mate1 similar by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Gut | Digestive System | |||||||||||||||||||||
| 32924 | 32924 | SRR29498568 | SRX25008884 | SRS21709103 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | F1g | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F1g|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 09 | 09 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | F1g_R1.fq.gz F1g_R2.fq.gz | fastq fastq | 8132653500.0 | 27108845.0 | F1g R1.fq.gz | 0:150 1:150 | A:1811779602;C:2095863397;G:2529881799;T:1695036688;N:92014 | 150 | 150 | 1811779602 | 2095863397 | 2529881799 | 1695036688 | 92014 | SRX25008884 | SRS21709103 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.53909 | 0.24181 | 0.01966 | 0.04797 | 0.99598 | 0.99624 | 0.59302 | 0.62038 | 150 | 150 | B | B | mate2-mate1 similar by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Gut | Digestive System | |||||||||||||||||||||
| 32925 | 32925 | SRR29498569 | SRX25008883 | SRS21709102 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | M2l | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:liver|identifier:M2l|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 08 | 08 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | M2l_R1.fq.gz M2l_R2.fq.gz | fastq fastq | 7733826600.0 | 25779422.0 | M2l R1.fq.gz | 0:150 1:150 | A:1754773283;C:2022716836;G:2330439864;T:1625790112;N:106505 | 150 | 150 | 1754773283 | 2022716836 | 2330439864 | 1625790112 | 106505 | SRX25008883 | SRS21709102 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.60941 | 0.31539 | 0.0377 | 0.09053 | 0.995 | 0.99478 | 0.50937 | 0.57123 | 150 | 150 | B | B | mate2-mate1 similar by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||
| 32926 | 32926 | SRR29498570 | SRX25008882 | SRS21709101 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | M2b | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M2b|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 07 | 07 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | M2b_R1.fq.gz M2b_R2.fq.gz | fastq fastq | 9324874800.0 | 31082916.0 | M2b R1.fq.gz | 0:150 1:150 | A:2073617286;C:2382074775;G:2948687855;T:1920389281;N:105603 | 150 | 150 | 2073617286 | 2382074775 | 2948687855 | 1920389281 | 105603 | SRX25008882 | SRS21709101 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.57388 | 0.29571 | 0.04187 | 0.10168 | 0.99506 | 0.99513 | 0.61677 | 0.60641 | 150 | 150 | B | B | mate2-mate1 similar by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Brain | Nervous System | |||||||||||||||||||||
| 32927 | 32927 | SRR29498571 | SRX25008881 | SRS21709100 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | M1l | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:liver|identifier:M1l|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 06 | 06 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | M1l_R2.fq.gz M1l_R1.fq.gz | fastq fastq | 8301268800.0 | 27670896.0 | M1l R1.fq.gz | 0:150 1:150 | A:1856070257;C:2266693166;G:2413641098;T:1764769457;N:94822 | 150 | 150 | 1856070257 | 2266693166 | 2413641098 | 1764769457 | 94822 | SRX25008881 | SRS21709100 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.8289 | 0.73852 | 0.21964 | 0.50932 | 0.99648 | 0.99701 | 0.57332 | 0.51129 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||
| 32928 | 32928 | SRR29498572 | SRX25008880 | SRS21709099 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | M1b | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M1b|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 05 | 05 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | M1b_R1.fq.gz M1b_R2.fq.gz | fastq fastq | 7947472800.0 | 26491576.0 | M1b R1.fq.gz | 0:150 1:150 | A:1764190500;C:1937842699;G:2595509352;T:1649839967;N:90282 | 150 | 150 | 1764190500 | 1937842699 | 2595509352 | 1649839967 | 90282 | SRX25008880 | SRS21709099 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.96542 | 0.21476 | 0.17288 | 0.05982 | 0.97289 | 0.99711 | 0.57845 | 0.611 | 150 | 150 | B | T | mate2 technical by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Brain | Nervous System | |||||||||||||||||||||
| 32929 | 32929 | SRR29498573 | SRX25008879 | SRS21709098 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | F2l | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F2l|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 04 | 04 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | F2l_R1.fq.gz F2l_R2.fq.gz | fastq fastq | 8701893900.0 | 29006313.0 | F2l R1.fq.gz | 0:150 1:150 | A:1977580339;C:2299061131;G:2585058451;T:1840095650;N:98329 | 150 | 150 | 1977580339 | 2299061131 | 2585058451 | 1840095650 | 98329 | SRX25008879 | SRS21709098 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.72425 | 0.57704 | 0.15111 | 0.37121 | 0.99744 | 0.99762 | 0.61161 | 0.55762 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||
| 32930 | 32930 | SRR29498574 | SRX25008878 | SRS21709097 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | F2b | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F2b|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 03 | 03 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | F2b_R1.fq.gz F2b_R2.fq.gz | fastq fastq | 9249410100.0 | 30831367.0 | F2b R1.fq.gz | 0:150 1:150 | A:2101671138;C:2272479255;G:2931272789;T:1943881150;N:105768 | 150 | 150 | 2101671138 | 2272479255 | 2931272789 | 1943881150 | 105768 | SRX25008878 | SRS21709097 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.96654 | 0.19343 | 0.23127 | 0.08081 | 0.95272 | 0.99326 | 0.63762 | 0.64901 | 150 | 150 | B | T | mate2 technical by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Brain | Nervous System | |||||||||||||||||||||
| 32931 | 32931 | SRR29498575 | SRX25008877 | SRS21709096 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | M2g | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M2g|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 12 | 12 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | M2g_R1.fq.gz M2g_R2.fq.gz | fastq fastq | 7106243100.0 | 23687477.0 | M2g R1.fq.gz | 0:150 1:150 | A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045 | 150 | 150 | 1567154123 | 1866065312 | 2213286944 | 1459656676 | 80045 | SRX25008877 | SRS21709096 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.56476 | 0.25026 | 0.02259 | 0.04481 | 0.99667 | 0.99701 | 0.63277 | 0.65693 | 150 | 150 | B | B | mate2-mate1 similar by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Gut | Digestive System | |||||||||||||||||||||
| 32932 | 32932 | SRR29498576 | SRX25008876 | SRS21709095 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | M1g | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 11 | 11 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | M1g_R2.fq.gz M1g_R1.fq.gz | fastq fastq | 7351182000.0 | 24503940.0 | M1g R1.fq.gz | 0:150 1:150 | A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321 | 150 | 150 | 1623685246 | 1858847576 | 2315396486 | 1553169371 | 83321 | SRX25008876 | SRS21709095 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.96004 | 0.21521 | 0.16113 | 0.04578 | 0.92431 | 0.99143 | 0.61867 | 0.63432 | 150 | 150 | B | T | mate2 technical by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Gut | Digestive System | |||||||||||||||||||||
| 32933 | 32933 | SRR29498577 | SRX25008875 | SRS21709094 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | F1l | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F1l|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 02 | 02 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | F1l_R2.fq.gz F1l_R1.fq.gz | fastq fastq | 4647564000.0 | 15491880.0 | F1l R1.fq.gz | 0:150 1:150 | A:993332389;C:862184908;G:1814249126;T:977710185;N:87392 | 150 | 150 | 993332389 | 862184908 | 1814249126 | 977710185 | 87392 | SRX25008875 | SRS21709094 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.88683 | 0.14922 | 0.24654 | 0.08178 | 0.9583 | 0.99819 | 0.70978 | 0.20254 | 150 | 150 | B | T | mate2 technical by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||
| 32934 | 32934 | SRR29498578 | SRX25008874 | SRS21709093 | SRP515416 | PRJNA1127032 | Zebrafish Tissue Mid Range RNA Sequencing | PRJNA1127032 | Other | This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples. | F1b | strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F1b|BioSampleModel:Model organism or animal | midRNA seq Danio rerio | 01 | 01 | Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP515416 | F1b_R2.fq.gz F1b_R1.fq.gz | fastq fastq | 7995852300.0 | 26652841.0 | F1b R1.fq.gz | 0:150 1:150 | A:1744452113;C:2053788787;G:2580416325;T:1617104387;N:90688 | 150 | 150 | 1744452113 | 2053788787 | 2580416325 | 1617104387 | 90688 | SRX25008874 | SRS21709093 | SRA1905460 | Eotvos Lorand University|Genetics | Eotvos Lorand University | 2 | 0.96107 | 0.17798 | 0.16452 | 0.02921 | 0.96759 | 0.99677 | 0.66455 | 0.62672 | 150 | 150 | B | T | mate2 technical by mapping diff | illumina | novaseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | Hungary | 2024-06-22 | Adult | Adult | Brain | Nervous System | |||||||||||||||||||||
| 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 | ||||||||||||||||
| 36271 | 36271 | SRR298568 | SRX079846 | SRS212652 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | ZiwiIPTes | GSM727525 | tissue:RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract|strain:TL | ZiwiIPTes | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract | Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Ziwi antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727525 | GSM727525: ZiwiIPTes | GSM727525: ZiwiIPTes | GSM727525: ZiwiIPTes | 1 | GEO Accession:GSM727525 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP007331 | read name barcode proc directive:ignore | ZiwiIPTes.fastq | fastq | 976120596.0 | 27114461.0 | GSM727525 1 | 0:36 | 36 | SRX079846 | SRS212652 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.10415 | 0.03658 | 0.96173 | 0.30033 | 36 | B | usable mapping rate | illumina | early_illumina | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Undetermined | Undetermined | Multi-tissue | Multi-system | |||||||||||||||||||||||
| 36272 | 36272 | SRR298567 | SRX079845 | SRS212651 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | ZiliIPTes | GSM727524 | tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL | ZiliIPTes | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | RNA obtained from immunoprecipitation with Zili antibody | Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727524 | GSM727524: ZiliIPTes | GSM727524: ZiliIPTes | GSM727524: ZiliIPTes | 1 | GEO Accession:GSM727524 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP007331 | read name barcode proc directive:ignore | ZiliIPTes.fastq | fastq | 995759064.0 | 27659974.0 | GSM727524 1 | 0:36 | 36 | SRX079845 | SRS212651 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.0537 | 0.03117 | 0.95856 | 0.42091 | 36 | B | usable mapping rate | illumina | early_illumina | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Undetermined | Undetermined | Trunk | Surface Structure | |||||||||||||||||||||||
| 36273 | 36273 | SRR298566 | SRX079844 | SRS212650 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | WTTESTIS | GSM727523 | tissue:adult testis extract|strain:TL | WTTESTIS | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | adult testis extract | Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727523 | GSM727523: WTTESTIS | GSM727523: WTTESTIS | GSM727523: WTTESTIS | 1 | GEO Accession:GSM727523 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP007331 | read name barcode proc directive:ignore | WTTESTIS.fastq | fastq | 732997980.0 | 20361055.0 | GSM727523 1 | 0:36 | 36 | SRX079844 | SRS212650 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.08155 | 0.07176 | 0.97851 | 0.52359 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||
| 36274 | 36274 | SRR298565 | SRX079843 | SRS212649 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | WT3WK | GSM727522 | tissue:3 wpf whole gonads|strain:TL | WT3WK | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | 3 wpf whole gonads | Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727522 | GSM727522: WT3WK | GSM727522: WT3WK | GSM727522: WT3WK | 1 | GEO Accession:GSM727522 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP007331 | read name barcode proc directive:ignore | WT3WK.fastq | fastq | 365473116.0 | 10152031.0 | GSM727522 1 | 0:36 | 36 | SRX079843 | SRS212649 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.09055 | 0.0603 | 0.97798 | 0.44571 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Larval | Larval | Gonad | Reproductive System | |||||||||||||||||||||||
| 36275 | 36275 | SRR298564 | SRX079842 | SRS212648 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | TDRD1WK3 | GSM727521 | tissue:3 wpf tdrd1 mutant gonads|strain:TL | TDRD1WK3 | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | 3 wpf tdrd1 mutant gonads | Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727521 | GSM727521: TDRD1WK3 | GSM727521: TDRD1WK3 | GSM727521: TDRD1WK3 | 1 | GEO Accession:GSM727521 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP007331 | read name barcode proc directive:ignore | TDRD1WK3.fastq | fastq | 369931536.0 | 10275876.0 | GSM727521 1 | 0:36 | 36 | SRX079842 | SRS212648 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.08303 | 0.04674 | 0.97938 | 0.35673 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Larval | Larval | Gonad | Reproductive System | |||||||||||||||||||||||
| 36276 | 36276 | SRR298563 | SRX079841 | SRS212647 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | TDRD1IPshort | GSM727520 | tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL | TDRD1IPshort | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract | Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Tdrd1 antibody 1:100 in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727520 | GSM727520: TDRD1IPshort | GSM727520: TDRD1IPshort | GSM727520: TDRD1IPshort | 1 | GEO Accession:GSM727520 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP007331 | read name barcode proc directive:ignore | TDRD1IPshort.fastq | fastq | 957724884.0 | 26603469.0 | GSM727520 1 | 0:36 | 36 | SRX079841 | SRS212647 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.10539 | 0.05124 | 0.93935 | 0.34909 | 36 | B | usable mapping rate | illumina | early_illumina | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Undetermined | Undetermined | Multi-tissue | Multi-system | |||||||||||||||||||||||
| 36277 | 36277 | SRR298562 | SRX079840 | SRS212646 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | TDRD1IPlong | GSM727519 | tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL | TDRD1IPlong | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract | Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Tdrd1 antibody 1:100 in a total volume of 500 µl. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727519 | GSM727519: TDRD1IPlong | GSM727519: TDRD1IPlong | GSM727519: TDRD1IPlong | 1 | GEO Accession:GSM727519 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</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> | SRP007331 | read name barcode proc directive:ignore | TDRD1IPlong.fastq | fastq | 1098157770.0 | 23872995.0 | GSM727519 1 | 0:46 | 46 | SRX079840 | SRS212646 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.63282 | 0.29001 | 0.80095 | 0.51046 | 46 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Undetermined | Undetermined | Multi-tissue | Multi-system | |||||||||||||||||||||||
| 36278 | 36278 | SRR352486 | SRX100938 | SRS266977 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | 3P Seq Adult | GSM813764 | source name:mixed gender adults|tissue:whole adult|developmental stage:mixed gender adults|genotype:wt | 3P Seq Adult | Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924 | mixed gender adults | For adult fish anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html | Zebrafish embryos or adults grown under standard condition | tissue:whole adult|developmental stage:mixed gender adults|genotype:wt | GSM813764 | GSM813764: 3P Seq Adult | GSM813764: 3P Seq Adult | GSM813764: 3P Seq Adult | 1 | GEO Accession:GSM813764 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | 3P_Seq_Adult.fastq | fastq | 824962572.0 | 22915627.0 | GSM813764 1 | 0:36 | A:230176177;C:144743199;G:130818857;T:314618483;N:4605856 | 36 | 230176177 | 144743199 | 130818857 | 314618483 | 4605856 | SRX100938 | SRS266977 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | 1 | 0.64306 | 0.03985 | 0.78102 | 0.46237 | 36 | B | usable mapping rate | illumina | early_illumina | 3prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Adult | Adult | Whole Organism | All anatomical structures | |||||||||||||||
| 36279 | 36279 | SRR352485 | SRX100937 | SRS266976 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | 3P Seq 72 hpf | GSM813763 | tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf | 3P Seq 72 hpf | Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924 | whole embryo at 72 hpf | Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html | Zebrafish embryos or adults grown under standard condition | tissue:whole embryo|developmental stage:72 hpf | GSM813763 | GSM813763: 3P Seq 72 hpf | GSM813763: 3P Seq 72 hpf | GSM813763: 3P Seq 72 hpf | 1 | GEO Accession:GSM813763 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | 3P_Seq_72hpf.fastq | fastq | 875542968.0 | 24320638.0 | GSM813763 1 | 0:36 | A:246098313;C:139311840;G:129654215;T:353566279;N:6912321 | 36 | 246098313 | 139311840 | 129654215 | 353566279 | 6912321 | SRX100937 | SRS266976 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | 1 | 0.72092 | 0.09355 | 0.7601 | 0.4422 | 36 | B | usable mapping rate | illumina | early_illumina | 3prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||
| 36280 | 36280 | SRR352484 | SRX100936 | SRS266975 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | 3P Seq 24 hpf | GSM813762 | tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf | 3P Seq 24 hpf | Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 | whole embryo at 24 hpf | Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html | Zebrafish embryos or adults grown under standard condition | tissue:whole embryo|developmental stage:24 hpf | GSM813762 | GSM813762: 3P Seq 24 hpf | GSM813762: 3P Seq 24 hpf | GSM813762: 3P Seq 24 hpf | 1 | GEO Accession:GSM813762 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | 3P_Seq_24hpf.fastq | fastq | 951095592.0 | 26419322.0 | GSM813762 1 | 0:36 | A:261158914;C:169001356;G:163312440;T:350565754;N:7057128 | 36 | 261158914 | 169001356 | 163312440 | 350565754 | 7057128 | SRX100936 | SRS266975 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | B | usable mapping rate | illumina | early_illumina | 3prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 36281 | 36281 | SRR352482 | SRX100935 | SRS266974 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | Strand specific RNA Seq 72 hpf | GSM813761 | tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf | Strand specific RNA Seq 72 hpf | Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches. | whole embryo at 72 hpf | Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992 | Zebrafish embryos or adults grown under standard condition | tissue:whole embryo|developmental stage:72 hpf | GSM813761 | GSM813761: Strand specific RNA Seq 72 hpf | GSM813761: Strand specific RNA Seq 72 hpf | GSM813761: Strand specific RNA Seq 72 hpf | 1 | GEO Accession:GSM813761 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | RNA_Seq_72hpf.1.fastq | fastq | 734147136.0 | 20392976.0 | GSM813761 1 | 0:36 | A:175662892;C:172216317;G:208650086;T:171852136;N:5765705 | 36 | 175662892 | 172216317 | 208650086 | 171852136 | 5765705 | SRX100935 | SRS266974 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | 1 | 0.4603 | 0.10593 | 0.88274 | 0.59195 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||
| 36282 | 36282 | SRR352483 | SRX100935 | SRS266974 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | Strand specific RNA Seq 72 hpf | GSM813761 | tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf | Strand specific RNA Seq 72 hpf | Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches. | whole embryo at 72 hpf | Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992 | Zebrafish embryos or adults grown under standard condition | tissue:whole embryo|developmental stage:72 hpf | GSM813761 | GSM813761: Strand specific RNA Seq 72 hpf | GSM813761: Strand specific RNA Seq 72 hpf | GSM813761: Strand specific RNA Seq 72 hpf | 1 | GEO Accession:GSM813761 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | RNA_Seq_72hpf.2.fastq | fastq | 924879168.0 | 25691088.0 | GSM813761 2 | 0:36 | A:218871678;C:217000200;G:266487098;T:214411336;N:8108856 | 36 | 218871678 | 217000200 | 266487098 | 214411336 | 8108856 | SRX100935 | SRS266974 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | 1 | 0.47296 | 0.10988 | 0.86397 | 0.59423 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||
| 36283 | 36283 | SRR352480 | SRX100934 | SRS266973 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | Strand specific RNA Seq 24 hpf | GSM813760 | tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf | Strand specific RNA Seq 24 hpf | Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches. | whole embryo at 24 hpf | Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992 | Zebrafish embryos or adults grown under standard condition | tissue:whole embryo|developmental stage:24 hpf | GSM813760 | GSM813760: Strand specific RNA Seq 24 hpf | GSM813760: Strand specific RNA Seq 24 hpf | GSM813760: Strand specific RNA Seq 24 hpf | 1 | GEO Accession:GSM813760 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | RNA_Seq_24hpf.1.fastq | fastq | 759129588.0 | 21086933.0 | GSM813760 1 | 0:36 | A:169759696;C:187766678;G:221392768;T:174382883;N:5827563 | 36 | 169759696 | 187766678 | 221392768 | 174382883 | 5827563 | SRX100934 | SRS266973 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | 1 | 0.52959 | 0.10037 | 0.87014 | 0.61896 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 36284 | 36284 | SRR352481 | SRX100934 | SRS266973 | SRP008845 | PRJNA146609 | Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution | GSE32880 | Other | Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome | pubmed:22196729 | Strand specific RNA Seq 24 hpf | GSM813760 | tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf | Strand specific RNA Seq 24 hpf | Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches. | whole embryo at 24 hpf | Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C. | polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992 | Zebrafish embryos or adults grown under standard condition | tissue:whole embryo|developmental stage:24 hpf | GSM813760 | GSM813760: Strand specific RNA Seq 24 hpf | GSM813760: Strand specific RNA Seq 24 hpf | GSM813760: Strand specific RNA Seq 24 hpf | 1 | GEO Accession:GSM813760 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <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> | SRP008845 | read name barcode proc directive:ignore | RNA_Seq_24hpf.2.fastq | fastq | 916505136.0 | 25458476.0 | GSM813760 2 | 0:36 | A:203678661;C:227621613;G:269472018;T:207401580;N:8331264 | 36 | 203678661 | 227621613 | 269472018 | 207401580 | 8331264 | SRX100934 | SRS266973 | SRA047033 | GEO | Whitehead Institute for Biomedical Research | 1 | 0.54008 | 0.10064 | 0.85425 | 0.61991 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2011-10-11 | Pharyngula | Embryo | Whole Organism | 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 | |||||||||||||||||
| 36335 | 36335 | SRR398322 | SRX115580 | SRS285697 | 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 | miRNA GFP minus | GSM861784 | source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types | miRNA GFP minus | The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. | whole zebrafish embryos at 24 hpf | 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. | age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types | GSM861784 | GSM861784: miRNA GFP minus; Danio rerio; RNA Seq | GSM861784 1 | GSM861784: miRNA GFP minus | 1 | GEO Accession:GSM861784 | 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_CNTL_WT.fastq.gz | fastq | 295021332.0 | 8195037.0 | GSM861784 r1 | 0:36 | A:70414178;C:53495749;G:76994313;T:87833261;N:6283831 | 36 | 70414178 | 53495749 | 76994313 | 87833261 | 6283831 | SRX115580 | SRS285697 | SRA049243 | GEO | Nathan Lawson Lab, PGFE, Umass Medical School | 1 | 0.02832 | 0.02716 | 0.99957 | 0.43137 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-01-12 | Pharyngula | Embryo | Trunk | Surface Structure | |||||||||||||||||
| 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 | ||||||||||||||||||||||
| 36514 | 36514 | SRR578923 | SRX190981 | SRS366702 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJD male | GSM1014087 | source name:Testes|sex:male|strain:SJD|development stage:Adult|tissue:Testes | SJD male | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Testes | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:male|strain:SJD|developmental stage:Adult|tissue:Testes | GSM1014087 | GSM1014087: SJD male; Danio rerio; RNA Seq | GSM1014087 1 | 1 | GEO Accession:GSM1014087 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | SJD_Male.fastq | fastq | 869956128.0 | 24165448.0 | GSM1014087 r1 | 0:36 | A:216078167;C:187750746;G:231408128;T:234642875;N:76212 | 36 | 216078167 | 187750746 | 231408128 | 234642875 | 76212 | SRX190981 | SRS366702 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.27444 | 0.19385 | 0.92478 | 0.49214 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36515 | 36515 | SRR578922 | SRX190980 | SRS366701 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | Tu Male | GSM1014086 | source name:Testes|sex:male|strain:Tu|development stage:Adult|tissue:Testes | Tu Male | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Testes | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:male|strain:Tu|developmental stage:Adult|tissue:Testes | GSM1014086 | GSM1014086: Tu Male; Danio rerio; RNA Seq | GSM1014086 1 | 1 | GEO Accession:GSM1014086 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 908421696.0 | 25233936.0 | GSM1014086 r1 | 0:36 | A:222765185;C:198165182;G:240641436;T:246807325;N:42568 | 36 | 222765185 | 198165182 | 240641436 | 246807325 | 42568 | SRX190980 | SRS366701 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.1451 | 0.10199 | 0.95128 | 0.45517 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36516 | 36516 | SRR578921 | SRX190979 | SRS366700 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF2 Individual 2 | GSM1014085 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF2 Individual 2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014085 | GSM1014085: TuxSJDF2 Individual 2; Danio rerio; RNA Seq | GSM1014085 1 | 1 | GEO Accession:GSM1014085 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 383509188.0 | 10653033.0 | GSM1014085 r1 | 0:36 | A:105355133;C:85084746;G:89408418;T:103592177;N:68714 | 36 | 105355133 | 85084746 | 89408418 | 103592177 | 68714 | SRX190979 | SRS366700 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.14582 | 0.10997 | 0.96175 | 0.35151 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36517 | 36517 | SRR578920 | SRX190978 | SRS366699 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF2 Individual 1 | GSM1014084 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF2 Individual 1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014084 | GSM1014084: TuxSJDF2 Individual 1; Danio rerio; RNA Seq | GSM1014084 1 | 1 | GEO Accession:GSM1014084 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | TuxSJDF1_Individual_1.fastq | fastq | 464899752.0 | 12913882.0 | GSM1014084 r1 | 0:36 | A:140830427;C:93401413;G:113254459;T:117332119;N:81334 | 36 | 140830427 | 93401413 | 113254459 | 117332119 | 81334 | SRX190978 | SRS366699 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.43194 | 0.32 | 0.93154 | 0.3438 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36518 | 36518 | SRR578919 | SRX190977 | SRS366698 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF2 | GSM1014083 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014083 | GSM1014083: TuxSJDF2; Danio rerio; RNA Seq | GSM1014083 1 | 1 | GEO Accession:GSM1014083 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | TuxSJDF2.fastq | fastq | 1036162620.0 | 28782295.0 | GSM1014083 r1 | 0:36 | A:268457303;C:215700792;G:273583173;T:278046713;N:374639 | 36 | 268457303 | 215700792 | 273583173 | 278046713 | 374639 | SRX190977 | SRS366698 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.16399 | 0.12914 | 0.9517 | 0.52232 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36519 | 36519 | SRR578918 | SRX190976 | SRS366697 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF1 Individual 2 | GSM1014082 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF1 Individual 2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014082 | GSM1014082: TuxSJDF1 Individual 2; Danio rerio; RNA Seq | GSM1014082 1 | 1 | GEO Accession:GSM1014082 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 344764980.0 | 9576805.0 | GSM1014082 r1 | 0:36 | A:90252809;C:80943703;G:83338280;T:90171695;N:58493 | 36 | 90252809 | 80943703 | 83338280 | 90171695 | 58493 | SRX190976 | SRS366697 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.18861 | 0.14536 | 0.95335 | 0.54431 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36520 | 36520 | SRR578917 | SRX190975 | SRS366696 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF1 Individual 1 | GSM1014081 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF1 Individual 1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014081 | GSM1014081: TuxSJDF1 Individual 1; Danio rerio; RNA Seq | GSM1014081 1 | 1 | GEO Accession:GSM1014081 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | TuxSJDF2_Individual_1.fastq | fastq | 373504320.0 | 10375120.0 | GSM1014081 r1 | 0:36 | A:96550943;C:89937876;G:87356943;T:99426239;N:232319 | 36 | 96550943 | 89937876 | 87356943 | 99426239 | 232319 | SRX190975 | SRS366696 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.15362 | 0.12272 | 0.95943 | 0.56453 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36521 | 36521 | SRR578916 | SRX190974 | SRS366695 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF1 | GSM1014080 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014080 | GSM1014080: TuxSJDF1; Danio rerio; RNA Seq | GSM1014080 1 | 1 | GEO Accession:GSM1014080 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | TuxSJDF1.fastq | fastq | 1031108904.0 | 28641914.0 | GSM1014080 r1 | 0:36 | A:270773113;C:213123466;G:267237418;T:279702377;N:272530 | 36 | 270773113 | 213123466 | 267237418 | 279702377 | 272530 | SRX190974 | SRS366695 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.15469 | 0.12537 | 0.95457 | 0.48819 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36522 | 36522 | SRR578915 | SRX190973 | SRS366694 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | Tu P0 Individual 2 | GSM1014079 | source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary | Tu P0 Individual 2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary | GSM1014079 | GSM1014079: Tu P0 Individual 2; Danio rerio; RNA Seq | GSM1014079 1 | 1 | GEO Accession:GSM1014079 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 464586408.0 | 12905178.0 | GSM1014079 r1 | 0:36 | A:150621423;C:99131637;G:92380585;T:122374816;N:77947 | 36 | 150621423 | 99131637 | 92380585 | 122374816 | 77947 | SRX190973 | SRS366694 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.0937 | 0.05289 | 0.96546 | 0.60026 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36523 | 36523 | SRR578914 | SRX190972 | SRS366693 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | Tu P0 Individual 1 | GSM1014078 | source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary | Tu P0 Individual 1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary | GSM1014078 | GSM1014078: Tu P0 Individual 1; Danio rerio; RNA Seq | GSM1014078 1 | 1 | GEO Accession:GSM1014078 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 427172796.0 | 11865911.0 | GSM1014078 r1 | 0:36 | A:135500495;C:91385480;G:87823245;T:112202150;N:261426 | 36 | 135500495 | 91385480 | 87823245 | 112202150 | 261426 | SRX190972 | SRS366693 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.1368 | 0.09652 | 0.95142 | 0.49555 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36524 | 36524 | SRR578913 | SRX190971 | SRS366692 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | Tu P0 | GSM1014077 | source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary | Tu P0 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary | GSM1014077 | GSM1014077: Tu P0; Danio rerio; RNA Seq | GSM1014077 1 | 1 | GEO Accession:GSM1014077 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 967772772.0 | 26882577.0 | GSM1014077 r1 | 0:36 | A:227085973;C:218180545;G:249458631;T:273002038;N:45585 | 36 | 227085973 | 218180545 | 249458631 | 273002038 | 45585 | SRX190971 | SRS366692 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.14418 | 0.1135 | 0.95818 | 0.51074 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36525 | 36525 | SRR578912 | SRX190970 | SRS366691 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJDxTuF2 Individual 2 | GSM1014076 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | SJDxTuF2 Individual 2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014076 | GSM1014076: SJDxTuF2 Individual 2; Danio rerio; RNA Seq | GSM1014076 1 | 1 | GEO Accession:GSM1014076 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 347475024.0 | 9652084.0 | GSM1014076 r1 | 0:36 | A:91189258;C:81789488;G:84551251;T:89882775;N:62252 | 36 | 91189258 | 81789488 | 84551251 | 89882775 | 62252 | SRX190970 | SRS366691 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.15872 | 0.12439 | 0.95848 | 0.56717 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36526 | 36526 | SRR578911 | SRX190969 | SRS366690 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJDxTuF2 Individual 1 | GSM1014075 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | SJDxTuF2 Individual 1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014075 | GSM1014075: SJDxTuF2 Individual 1; Danio rerio; RNA Seq | GSM1014075 1 | 1 | GEO Accession:GSM1014075 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 400137228.0 | 11114923.0 | GSM1014075 r1 | 0:36 | A:107143937;C:91495000;G:94706504;T:106722021;N:69766 | 36 | 107143937 | 91495000 | 94706504 | 106722021 | 69766 | SRX190969 | SRS366690 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.15753 | 0.12463 | 0.95538 | 0.5649 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36527 | 36527 | SRR578910 | SRX190968 | SRS366689 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJDxTuF2 | GSM1014074 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | SJDxTuF2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014074 | GSM1014074: SJDxTuF2; Danio rerio; RNA Seq | GSM1014074 1 | 1 | GEO Accession:GSM1014074 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | SJDxTuF2.fastq | fastq | 958492116.0 | 26624781.0 | GSM1014074 r1 | 0:36 | A:261275440;C:193944805;G:248348765;T:254793050;N:130056 | 36 | 261275440 | 193944805 | 248348765 | 254793050 | 130056 | SRX190968 | SRS366689 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.20051 | 0.16387 | 0.94653 | 0.53263 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36528 | 36528 | SRR578909 | SRX190967 | SRS366688 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJDxTuF1 Individual 2 | GSM1014073 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | SJDxTuF1 Individual 2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014073 | GSM1014073: SJDxTuF1 Individual 2; Danio rerio; RNA Seq | GSM1014073 1 | 1 | GEO Accession:GSM1014073 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 435761532.0 | 12104487.0 | GSM1014073 r1 | 0:36 | A:120580697;C:105605593;G:91379055;T:117787426;N:408761 | 36 | 120580697 | 105605593 | 91379055 | 117787426 | 408761 | SRX190967 | SRS366688 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.07215 | 0.05695 | 0.97557 | 0.48838 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36529 | 36529 | SRR578908 | SRX190966 | SRS366687 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJDxTuF1 Individual 1 | GSM1014072 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | SJDxTuF1 Individual 1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014072 | GSM1014072: SJDxTuF1 Individual 1; Danio rerio; RNA Seq | GSM1014072 1 | 1 | GEO Accession:GSM1014072 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 378296532.0 | 10508237.0 | GSM1014072 r1 | 0:36 | A:109216358;C:76585213;G:90165899;T:102085771;N:243291 | 36 | 109216358 | 76585213 | 90165899 | 102085771 | 243291 | SRX190966 | SRS366687 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.13684 | 0.10794 | 0.96335 | 0.49651 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36530 | 36530 | SRR578907 | SRX190965 | SRS366686 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJDxTuF1 | GSM1014071 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | SJDxTuF1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014071 | GSM1014071: SJDxTuF1; Danio rerio; RNA Seq | GSM1014071 1 | 1 | GEO Accession:GSM1014071 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | 1047688380.0 | 29102455.0 | GSM1014071 r1 | 0:36 | A:277032474;C:213232299;G:269309034;T:288068877;N:45696 | 36 | 277032474 | 213232299 | 269309034 | 288068877 | 45696 | SRX190965 | SRS366686 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.1858 | 0.15153 | 0.95006 | 0.51345 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||
| 36531 | 36531 | SRR578906 | SRX190964 | SRS366685 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJD P0 Individual 2 | GSM1014070 | source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary | SJD P0 Individual 2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary | GSM1014070 | GSM1014070: SJD P0 Individual 2; Danio rerio; RNA Seq | GSM1014070 1 | 1 | GEO Accession:GSM1014070 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | SJD_P0_Individual_2.fastq | fastq | 392951772.0 | 10915327.0 | GSM1014070 r1 | 0:36 | A:126709476;C:82393458;G:82997127;T:100597122;N:254589 | 36 | 126709476 | 82393458 | 82997127 | 100597122 | 254589 | SRX190964 | SRS366685 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.12786 | 0.10199 | 0.95724 | 0.52026 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36532 | 36532 | SRR578905 | SRX190963 | SRS366684 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJD P0 Individual 1 | GSM1014069 | source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary | SJD P0 Individual 1 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary | GSM1014069 | GSM1014069: SJD P0 Individual 1; Danio rerio; RNA Seq | GSM1014069 1 | 1 | GEO Accession:GSM1014069 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | SJD_P0_Individual_1.fastq | fastq | 379882512.0 | 10552292.0 | GSM1014069 r1 | 0:36 | A:122444116;C:80302064;G:76948943;T:99839311;N:348078 | 36 | 122444116 | 80302064 | 76948943 | 99839311 | 348078 | SRX190963 | SRS366684 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.21364 | 0.16206 | 0.94268 | 0.45306 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36533 | 36533 | SRR578904 | SRX190962 | SRS366683 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | SJD P0 | GSM1014068 | source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary | SJD P0 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary | GSM1014068 | GSM1014068: SJD P0; Danio rerio; RNA Seq | GSM1014068 1 | 1 | GEO Accession:GSM1014068 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | SJD_P0.fastq | fastq | 837950832.0 | 23276412.0 | GSM1014068 r1 | 0:36 | A:217386642;C:179519865;G:217337232;T:223633685;N:73408 | 36 | 217386642 | 179519865 | 217337232 | 223633685 | 73408 | SRX190962 | SRS366683 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.26607 | 0.21631 | 0.93789 | 0.46928 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||
| 36731 | 36731 | SRR836199 | SRX272888 | SRS417394 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq 5dpf | GSM1131537 | tissue:Whole embryos|developmental stage:5 dpf molecule:ribosome footprinted RNA | 20120724 RPF Seq 5dpf | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:5 dpf molecule:ribosome footprinted RNA | GSM1131537 | GSM1131537: 20120724 RPF Seq 5dpf; Danio rerio; RNA Seq | GSM1131537 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131537 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_5dpf.fastq.gz | fastq | 5339394852.0 | 121349883.0 | GSM1131537 r1 | 0:44 | A:993131212;C:1552513636;G:1792926993;T:1000757523;N:65488 | 44 | 993131212 | 1552513636 | 1792926993 | 1000757523 | 65488 | SRX272888 | SRS417394 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.04708 | 0.00988 | 0.99774 | 0.7502 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||
| 36732 | 36732 | SRR836198 | SRX272887 | SRS417393 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq 28hpf | GSM1131536 | tissue:Whole embryos|developmental stage:28 hpf molecule:ribosome footprinted RNA | 20120724 RPF Seq 28hpf | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:28 hpf molecule:ribosome footprinted RNA | GSM1131536 | GSM1131536: 20120724 RPF Seq 28hpf; Danio rerio; RNA Seq | GSM1131536 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131536 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_28hpf.fastq.gz | fastq | 5844769480.0 | 132835670.0 | GSM1131536 r1 | 0:44 | A:967687923;C:1803414766;G:2048220630;T:1024594100;N:852061 | 44 | 967687923 | 1803414766 | 2048220630 | 1024594100 | 852061 | SRX272887 | SRS417393 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.054 | 0.00377 | 0.99762 | 0.77752 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 36733 | 36733 | SRR836197 | SRX272886 | SRS417392 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq Bud | GSM1131535 | tissue:Whole embryos|developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA | 20120724 RPF Seq Bud | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA | GSM1131535 | GSM1131535: 20120724 RPF Seq Bud; Danio rerio; RNA Seq | GSM1131535 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131535 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_Bud.fastq.gz | fastq | 5245678988.0 | 119219977.0 | GSM1131535 r1 | 0:44 | A:785136766;C:1705642298;G:1892015387;T:862815185;N:69352 | 44 | 785136766 | 1705642298 | 1892015387 | 862815185 | 69352 | SRX272886 | SRS417392 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.0214 | 0.00105 | 0.99823 | 0.906 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Undetermined | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 36734 | 36734 | SRR836196 | SRX272885 | SRS417391 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq Shield | GSM1131534 | tissue:Whole embryos|developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA | 20120724 RPF Seq Shield | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA | GSM1131534 | GSM1131534: 20120724 RPF Seq Shield; Danio rerio; RNA Seq | GSM1131534 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131534 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_Shield.fastq.gz | fastq | 5407148516.0 | 122889739.0 | GSM1131534 r1 | 0:44 | A:1112688703;C:1598204601;G:1639649897;T:1055648833;N:956482 | 44 | 1112688703 | 1598204601 | 1639649897 | 1055648833 | 956482 | SRX272885 | SRS417391 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.01533 | 0.0016 | 0.99864 | 0.73416 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Gastrula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 36735 | 36735 | SRR836195 | SRX272884 | SRS417390 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq Dome | GSM1131533 | tissue:Whole embryos|developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA | 20120724 RPF Seq Dome | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA | GSM1131533 | GSM1131533: 20120724 RPF Seq Dome; Danio rerio; RNA Seq | GSM1131533 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131533 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_Dome.fastq.gz | fastq | 5455941832.0 | 123998678.0 | GSM1131533 r1 | 0:44 | A:1174530251;C:1596486361;G:1605087499;T:1077423125;N:2414596 | 44 | 1174530251 | 1596486361 | 1605087499 | 1077423125 | 2414596 | SRX272884 | SRS417390 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.00739 | 0.0007 | 0.99898 | 0.86907 | 44 | T | under 1.2% mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 36736 | 36736 | SRR836194 | SRX272883 | SRS417389 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq 1KCell | GSM1131532 | tissue:Whole embryos|developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA | 20120724 RPF Seq 1KCell | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA | GSM1131532 | GSM1131532: 20120724 RPF Seq 1KCell; Danio rerio; RNA Seq | GSM1131532 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131532 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_1KCell.fastq.gz | fastq | 6177670620.0 | 140401605.0 | GSM1131532 r1 | 0:44 | A:1115906097;C:1874096579;G:1974799887;T:1211772717;N:1095340 | 44 | 1115906097 | 1874096579 | 1974799887 | 1211772717 | 1095340 | SRX272883 | SRS417389 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.02237 | 0.00392 | 0.99847 | 0.87194 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 36737 | 36737 | SRR836193 | SRX272882 | SRS417388 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq 256Cell | GSM1131531 | tissue:Whole embryos|developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA | 20120724 RPF Seq 256Cell | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA | GSM1131531 | GSM1131531: 20120724 RPF Seq 256Cell; Danio rerio; RNA Seq | GSM1131531 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131531 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_256Cell.fastq.gz | fastq | 5883566700.0 | 133717425.0 | GSM1131531 r1 | 0:44 | A:1010263447;C:1822722383;G:1960819573;T:1088614485;N:1146812 | 44 | 1010263447 | 1822722383 | 1960819573 | 1088614485 | 1146812 | SRX272882 | SRS417388 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.02862 | 0.0036 | 0.99837 | 0.90559 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 36738 | 36738 | SRR836192 | SRX272881 | SRS417387 | SRP021915 | PRJNA200706 | Ribosome Profiling over a Zebrafish Developmental Timecourse | GSE46512 | Transcriptome Analysis | To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | pubmed:23698349 | 20120724 RPF Seq 2 4Cell | GSM1131530 | tissue:Whole embryos|developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA | 20120724 RPF Seq 2 4Cell | Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | 400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA | GSM1131530 | GSM1131530: 20120724 RPF Seq 2 4Cell; Danio rerio; RNA Seq | GSM1131530 1 | 1 | Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011 | GEO Accession:GSM1131530 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP021915 | 20120724_RPF-Seq_2-4Cell.fastq.gz | fastq | 1568173420.0 | 35640305.0 | GSM1131530 r1 | 0:44 | A:256220962;C:489258424;G:538563811;T:283859833;N:270390 | 44 | 256220962 | 489258424 | 538563811 | 283859833 | 270390 | SRX272881 | SRS417387 | SRA075002 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 1 | 0.0297 | 0.00558 | 0.99821 | 0.89066 | 44 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | United States | 2013-04-30 | Cleavage | Embryo | Whole Organism | 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 |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;