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12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue_curation_coarse = "Surface Structure"

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tissue_curation 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Surface Structure · 12 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 12 ✖

experiment.library_layout 1

  • SINGLE · 12 ✖
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
125 125 DRR189379 DRX179844 DRS200410 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 3 SAMD00182222   sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182222 DRX179844 Emx3 / Larva body 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182222       1759409208.0 48872478.0 DRR189379 0:36 A:401147348;C:424523813;G:426350919;T:507310828;N:76300 36       401147348 424523813 426350919 507310828 76300 DRX179844 DRS200410 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90975   0.11439   0.66076   0.47775   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
126 126 DRR189378 DRX179843 DRS200409 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 2 SAMD00182221   sample name:Emx3 Larva body 2|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182221 DRX179843 Emx3 / Larva body 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182221       1318201020.0 36616695.0 DRR189378 0:36 A:297850068;C:316786585;G:323717530;T:379789606;N:57231 36       297850068 316786585 323717530 379789606 57231 DRX179843 DRS200409 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.9116   0.11269   0.65837   0.46733   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
127 127 DRR189377 DRX179842 DRS200408 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 1 SAMD00182220   sample name:Emx3 Larva body 1|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182220 DRX179842 Emx3 / Larva body 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182220       812483964.0 22568999.0 DRR189377 0:36 A:185173338;C:197790160;G:197482964;T:232000884;N:36618 36       185173338 197790160 197482964 232000884 36618 DRX179842 DRS200408 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91107   0.1171   0.65981   0.47458   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
128 128 DRR189376 DRX179841 DRS200449 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 3 SAMD00182219   sample name:WT Larva body 3|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182219 DRX179841 WT Larva body 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182219       4030038144.0 111945504.0 DRR189376 0:36 A:943709984;C:971756680;G:977594500;T:1136798448;N:178532 36       943709984 971756680 977594500 1136798448 178532 DRX179841 DRS200449 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89574   0.12331   0.65831   0.48096   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
129 129 DRR189375 DRX179840 DRS200448 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 2 SAMD00182218   sample name:WT Larva body 2|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182218 DRX179840 WT Larva body 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182218       1991670804.0 55324189.0 DRR189375 0:36 A:454367176;C:479012055;G:488407231;T:569793674;N:90668 36       454367176 479012055 488407231 569793674 90668 DRX179840 DRS200448 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90911   0.12455   0.65494   0.47971   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
130 130 DRR189374 DRX179839 DRS200447 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 1 SAMD00182217   sample name:WT Larva body 1|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182217 DRX179839 WT Larva body 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182217       1018340100.0 28287225.0 DRR189374 0:36 A:233370050;C:244140659;G:247795084;T:292989542;N:44765 36       233370050 244140659 247795084 292989542 44765 DRX179839 DRS200447 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91078   0.12578   0.6524   0.48016   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
38116 38116 SRR1551799 SRX681419 SRS685080 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       keratocytes from 4dpf embryos keratocytes from 4dpf embryos   breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal                 transcriptome from 4dpf keratocytes replicate 3 4dpf 3 4dpf 3 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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> SRP045504     lane4_4dpf707.fastq fastq 1001179200.0 25029480.0 4dpf 3 0:40 A:253770714;C:242097985;G:244642013;T:260557997;N:110491 40       253770714 242097985 244642013 260557997 110491 SRX681419 SRS685080 SRA179326 Stanford University|Julie Theriot Stanford University 1 0.90546   0.2101   0.75185   0.49242   40   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2015-04-07 Larval Larval Skin Surface Structure
38117 38117 SRR1551798 SRX681418 SRS685080 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       keratocytes from 4dpf embryos keratocytes from 4dpf embryos   breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal                 Transcriptome from 4dpf keratocytes replicate 2 4dpf 2 4dpf 2 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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> SRP045504     lane7_4col.fastq fastq 1700157430.0 44740985.0 4dpf 2 0:38 A:394789834;C:418821057;G:504852317;T:369111176;N:12583046 38       394789834 418821057 504852317 369111176 12583046 SRX681418 SRS685080 SRA179326 Stanford University|Julie Theriot Stanford University 1 0.68441   0.12529   0.8338   0.45494   38   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2014-08-14 Larval Larval Skin Surface Structure
38118 38118 SRR1551797 SRX681417 SRS685080 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       keratocytes from 4dpf embryos keratocytes from 4dpf embryos   breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal                 4dpf keratocyte transcriptome replicate 1 4dpf 1 4dpf 1 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>47</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> SRP045504     lane7_1_4dpf.fastq fastq 762138229.0 16215707.0 4dpf 1 0:47 A:183899711;C:180347476;G:190086042;T:189460942;N:18344058 47       183899711 180347476 190086042 189460942 18344058 SRX681417 SRS685080 SRA179326 Stanford University|Julie Theriot Stanford University 1 0.85884   0.2135   0.80077   0.50539   47   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2014-08-15 Larval Larval Skin Surface Structure
38119 38119 SRR1551796 SRX681416 SRS685079 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       Transcriptome from 2dpf keratocytes keratocytes from 2dpf embryos   breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal                 Transcriptome from 2dpf keratocytes replicate 3 2dpf 3 2dpf 3 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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> SRP045504     lane3_2dpf629.fastq fastq 551787520.0 13794688.0 2dpf 3 0:40 A:138660463;C:132605577;G:134640312;T:145852714;N:28454 40       138660463 132605577 134640312 145852714 28454 SRX681416 SRS685079 SRA179323 Stanford University|Julie Theriot Stanford University 1 0.91375   0.21598   0.75317   0.47881   40   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2014-08-14 Hatching Embryo Skin Surface Structure
38120 38120 SRR1551795 SRX681415 SRS685079 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       Transcriptome from 2dpf keratocytes keratocytes from 2dpf embryos   breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal                 Transcriptome from 2dpf keratocytes 2dpf 2 2dpf 2 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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> SRP045504     lane1_2dpf.fastq fastq 796874112.0 22135392.0 2dpf 2 0:36 A:209956517;C:184659684;G:185142987;T:216055902;N:1059022 36       209956517 184659684 185142987 216055902 1059022 SRX681415 SRS685079 SRA179323 Stanford University|Julie Theriot Stanford University 1 0.89178   0.17837   0.7609   0.49774   36   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2015-04-07 Hatching Embryo Skin Surface Structure
38121 38121 SRR1551782 SRX681402 SRS685079 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       Transcriptome from 2dpf keratocytes keratocytes from 2dpf embryos   breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal                 2dpf keratocytes replicate 1 2dpf 1 2dpf 1 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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> SRP045504     lane6_2dpf.fastq fastq 647944118.0 17051161.0 2dpf 1 0:38 A:145735255;C:167786338;G:186677806;T:141598169;N:6146550 38       145735255 167786338 186677806 141598169 6146550 SRX681402 SRS685079 SRA179323 Stanford University|Julie Theriot Stanford University 1 0.7695   0.15816   0.81491   0.44972   38   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2014-08-14 Hatching Embryo Skin Surface Structure

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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");;