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15 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "OTHER" and tissue_curation = "Undetermined"

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experiment.library_selection 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Undetermined · 15 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

  • OTHER · 15 ✖

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 15 ✖

devstage_curation_coarse 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29215 29215 SRR27489731 SRX23160978 SRS20111136 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     RNA product control RNA library RNA mMessage MPRA library   strain:not applicable|age:not applicable|dev stage:not applicable|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:not applicable|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:not applicable|growth protocol:not applicable|sample type:IVT mRNA|sample number:50|replicate:unique sample|BioSampleModel:Model organism or animal                 control RNA library Library 50 Library 50 PCR product was amplified from DNA plasmid pool with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R2_001_MM_1.fastq.gz fastq fastq 16695252486.0 55282293.0 BSSE QGF 206685 HGWLYDSX3 3 RNA mMessage MPRA library test GGTTATAA GATATCGA S50 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4275447149;C:4413405571;G:3936523108;T:4069049357;N:827301 151 151     4275447149 4413405571 3936523108 4069049357 827301 SRX23160978 SRS20111136 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02176 0.00021 0.00058 2e-05 0.99056 0.99933 0.41475 0.48571 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
37185 37185 SRR1010334 SRX363385 SRS490049 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL7F transgenic line   strain:AB strain MUTL7F line|development stage:high 3.3 hpf                 D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL7F_transgene_R1.fastq MUTL7F_transgene_R2.fastq fastq fastq 30678849.0 444621.0 D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:5994534;C:7452275;G:9596502;T:7623459;N:12079 34 35     5994534 7452275 9596502 7623459 12079 SRX363385 SRS490049 SRA104816 University of Bergen ZEPROME consortium 2 0.38487 0.37445 0.0013 9e-05 0.99841 0.99991 0.00309 0.00012 34 35 B B biological fallback assumption illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37186 37186 SRR1010333 SRX363384 SRS490049 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL7F transgenic line   strain:AB strain MUTL7F line|development stage:high 3.3 hpf                 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL7F_endogenous_R2.fastq MUTL7F_endogenous_R1.fastq fastq fastq 78367233.0 1135757.0 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:21010895;C:20506800;G:21883789;T:14935556;N:30193 34 35     21010895 20506800 21883789 14935556 30193 SRX363384 SRS490049 SRA104816 University of Bergen ZEPROME consortium 2 0.56643 0.02972 6e-05 0.00056 0.99965 0.99995 0.00017 0.05769 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37187 37187 SRR1010332 SRX363383 SRS490048 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL6F transgenic line   strain:AB strain MUTL6F line|development stage:high 3.3 hpf                 D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL6F_transgene_R2.fastq MUTL6F_transgene_R1.fastq fastq fastq 36838272.0 533888.0 D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:7267891;C:8939911;G:11513757;T:9101861;N:14852 34 35     7267891 8939911 11513757 9101861 14852 SRX363383 SRS490048 SRA104816 University of Bergen ZEPROME consortium 2 0.35237 0.20738 0.00196 4e-05 0.9991 0.99987 0.00131 0.00022 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37188 37188 SRR1010331 SRX363382 SRS490048 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL6F transgenic line   strain:AB strain MUTL6F line|development stage:high 3.3 hpf                 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL6F_endogenous_R1.fastq MUTL6F_endogenous_R2.fastq fastq fastq 67887582.0 983878.0 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:18224546;C:17687428;G:19119778;T:12829091;N:26739 34 35     18224546 17687428 19119778 12829091 26739 SRX363382 SRS490048 SRA104816 University of Bergen ZEPROME consortium 2 0.57761 0.02201 0.0001 0.00048 0.99975 0.99991 0.00011 0.02247 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37189 37189 SRR1010330 SRX363381 SRS490047 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL5F transgenic line   strain:AB strain MUTL5F line|development stage:high 3.3 hpf                 D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL5F_transgene_R1.fastq MUTL5F_transgene_R2.fastq fastq fastq 48750708.0 706532.0 D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:9468865;C:11866504;G:15193605;T:12203213;N:18521 34 35     9468865 11866504 15193605 12203213 18521 SRX363381 SRS490047 SRA104816 University of Bergen ZEPROME consortium 2 0.37677 0.39423 0.0018 0.00013 0.99801 0.99989 0.00295 0.00011 34 35 B B biological fallback assumption illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37190 37190 SRR1010329 SRX363380 SRS490047 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL5F transgenic line   strain:AB strain MUTL5F line|development stage:high 3.3 hpf                 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL5F_endogenous_R1.fastq MUTL5F_endogenous_R2.fastq fastq fastq 85325883.0 1236607.0 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:22831000;C:22316529;G:23804395;T:16340044;N:33915 34 35     22831000 22316529 23804395 16340044 33915 SRX363380 SRS490047 SRA104816 University of Bergen ZEPROME consortium 2 0.59785 0.01902 0.00632 0.00081 0.99941 0.99993 0.00056 0.11235 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37191 37191 SRR1010328 SRX363379 SRS490046 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL2F transgenic line   strain:AB strain MUTL2F line|development stage:high 3.3 hpf                 D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL2F_transgene_R1.fastq MUTL2F_transgene_R2.fastq fastq fastq 68247900.0 989100.0 D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:13037092;C:16853304;G:21557175;T:16772703;N:27626 34 35     13037092 16853304 21557175 16772703 27626 SRX363379 SRS490046 SRA104816 University of Bergen ZEPROME consortium 2 0.37746 0.14836 0.00135 0.00215 0.99912 0.99995 0.00128 0.0 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37192 37192 SRR1010327 SRX363378 SRS490046 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL2F transgenic line   strain:AB strain MUTL2F line|development stage:high 3.3 hpf                 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL2F_endogenous_R1.fastq MUTL2F_endogenous_R2.fastq fastq fastq 85300215.0 1236235.0 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:22860161;C:22364533;G:24027064;T:16015109;N:33348 34 35     22860161 22364533 24027064 16015109 33348 SRX363378 SRS490046 SRA104816 University of Bergen ZEPROME consortium 2 0.57324 0.0117 0.01138 0.00049 0.99943 0.99993 0.00087 0.02941 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37193 37193 SRR1010326 SRX363377 SRS490045 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL3F transgenic line   strain:AB strain WTL3F line|development stage:high 3.3 hpf                 D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL3F_transgene_R1.fastq WTL3F_transgene_R2.fastq fastq fastq 36051879.0 522491.0 D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:6990071;C:8680451;G:10883119;T:9484027;N:14211 34 35     6990071 8680451 10883119 9484027 14211 SRX363377 SRS490045 SRA104816 University of Bergen ZEPROME consortium 2 0.43354 0.14606 0.00247 9e-05 0.99896 0.99991 0.00217 0.00032 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37194 37194 SRR1010325 SRX363376 SRS490045 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL3F transgenic line   strain:AB strain WTL3F line|development stage:high 3.3 hpf                 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL3F_endogenous_R1.fastq WTL3F_endogenous_R2.fastq fastq fastq 78469284.0 1137236.0 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 0:34 1:35 A:21059562;C:20597989;G:21976657;T:14804744;N:30332 34 35     21059562 20597989 21976657 14804744 30332 SRX363376 SRS490045 SRA104816 University of Bergen ZEPROME consortium 2 0.54772 0.02239 3e-05 0.0 0.99979 0.99993 0.00012 0.06756 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37195 37195 SRR1010324 SRX363375 SRS490044 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL2F transgenic line   strain:AB strain WTL2F line|development stage:high 3.3 hpf                 D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL2F_transgene_R1.fastq WTL2F_transgene_R2.fastq fastq fastq 67052544.0 971776.0 D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:12413417;C:16491074;G:20506887;T:17614500;N:26666 34 35     12413417 16491074 20506887 17614500 26666 SRX363375 SRS490044 SRA104816 University of Bergen ZEPROME consortium 2 0.47234 0.16966 0.00033 0.00039 0.99918 0.99993 0.00051 0.0 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37196 37196 SRR1010323 SRX363374 SRS490044 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL2F transgenic line   strain:AB strain WTL2F line|development stage:high 3.3 hpf                 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL2F_endogenous_R1.fastq WTL2F_endogenous_R2.fastq fastq fastq 71493591.0 1036139.0 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 0:34 1:35 A:19123161;C:18705556;G:20092193;T:13545180;N:27501 34 35     19123161 18705556 20092193 13545180 27501 SRX363374 SRS490044 SRA104816 University of Bergen ZEPROME consortium 2 0.56581 0.02161 0.00279 0.00056 0.99949 0.99991 0.00025 0.09333 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37197 37197 SRR1010322 SRX363361 SRS490033 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL1F transgenic line   strain:AB strain WTL1F line|dev stage:high 3.3 hpf                 D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL1F_transgene_R1.fastq WTL1F_transgene_R2.fastq fastq fastq 95222070.0 1380030.0 D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:17371572;C:23537350;G:29495884;T:24779827;N:37437 34 35     17371572 23537350 29495884 24779827 37437 SRX363361 SRS490033 SRA104816 University of Bergen ZEPROME consortium 2 0.44573 0.30978 0.00036 0.00019 0.99943 0.99991 0.00023 0.00124 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37198 37198 SRR1010321 SRX363360 SRS490033 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL1F transgenic line   strain:AB strain WTL1F line|dev stage:high 3.3 hpf                 D. rerio WTL1F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL1F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL1F_endogenous_R1.fastq WTL1F_endogenous_R2.fastq fastq fastq 64955082.0 941378.0 D. rerio WTL1F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:17404375;C:16997013;G:18318738;T:12210960;N:23996 34 35     17404375 16997013 18318738 12210960 23996 SRX363360 SRS490033 SRA104816 University of Bergen ZEPROME consortium 2 0.55528 0.02138 9e-05 0.00135 0.99963 0.99991 9e-05 0.10169 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise

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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");;