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25 rows where experiment.library_layout = "PAIRED" and experiment.library_selection = "CAGE"

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devstage_curation 5

tissue_curation 4

experiment.library_strategy 2

devstage_curation_coarse 2

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • CAGE · 25 ✖

experiment.library_layout 1

  • PAIRED · 25 ✖
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
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
55270 55270 SRR10215486 SRX6935169 SRS5465204 SRP223930 PRJNA575342 CAGE /CappedRNA sequencig PRJNA575342 Other CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development         S06 Prim5   strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo Prim 5 stage Prim5 nAnTiCAGE Prim5 nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2500   SRP223930     S06_Prim5_nAnTiCAGE_1.fastq.gz S06_Prim5_nAnTiCAGE_2.fastq.gz fastq fastq 2672456099.0 13565767.0 S06 Prim5 nAnTiCAGE 1.fastq.gz 0:97 1:100 A:641958912;C:678208106;G:686299870;T:662301091;N:3688120 97 100     641958912 678208106 686299870 662301091 3688120 SRX6935169 SRS5465204 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 2 0.94637 0.95975 0.15027 0.16177 0.74119 0.7441 0.50314 0.54386 97 100 B B biological fallback assumption illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Pharyngula Embryo Whole Organism All anatomical structures
55271 55271 SRR10215487 SRX6935168 SRS5465203 SRP223930 PRJNA575342 CAGE /CappedRNA sequencig PRJNA575342 Other CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development         S05 4 Somies   strain:AB|dev stage:4 5 somites|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo 4 5 somites stage 4Somites nAnTiCAGE 4Somites nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2500   SRP223930     S05_4Somites_nAnTiCAGE_1.fastq.gz S05_4Somites_nAnTiCAGE_2.fastq.gz fastq fastq 1532850499.0 7780967.0 S05 4Somites nAnTiCAGE 1.fastq.gz 0:97 1:100 A:368505591;C:387404999;G:393120996;T:381726796;N:2092117 97 100     368505591 387404999 393120996 381726796 2092117 SRX6935168 SRS5465203 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 2 0.93818 0.96364 0.10425 0.1218 0.75116 0.74852 0.54456 0.54636 97 100 B B biological fallback assumption illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Segmentation Embryo Whole Organism All anatomical structures
55275 55275 SRR10215491 SRX6935164 SRS5465199 SRP223930 PRJNA575342 CAGE /CappedRNA sequencig PRJNA575342 Other CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development         S01 1Cell   strain:AB|dev stage:1cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo 1 cell stage 1Cell nAnTiCAGE 1Cell nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2500   SRP223930     S01_1Cells_nAnTiCAGE_1.fastq.gz S01_1Cells_nAnTiCAGE_2.fastq.gz fastq fastq 1193891117.0 6060361.0 S01 1Cells nAnTiCAGE 1.fastq.gz 0:97 1:100 A:286037352;C:298140071;G:310668851;T:297430066;N:1614777 97 100     286037352 298140071 310668851 297430066 1614777 SRX6935164 SRS5465199 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 2 0.93733 0.97059 0.08219 0.07881 0.76682 0.75834 0.53879 0.54537 97 100 B B biological fallback assumption illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Zygote Embryo Whole Organism All anatomical structures
68254 68254 SRR18327318 SRX14464504 SRS11744581 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow nanoCAGE zebrafish TU testis rep2 nanoCAGE zebrafish TU testis rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_testis_BR2.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR2.R2.fastq.gz fastq fastq 2408261400.0 15886644.0 nano TUzfish combined deep testis BR2.R1.fastq.gz 0:75.80 1:75.80 A:589293804;C:562741604;G:604867589;T:650872884;N:485519 75 75     589293804 562741604 604867589 650872884 485519 SRX14464504 SRS11744581 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.05991 0.93925 0.00631 0.04834 0.91364 0.67671 0.54402 0.49323 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Gonad Reproductive System
68255 68255 SRR18327319 SRX14464503 SRS11744582 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow nanoCAGE zebrafish TU testis rep1 nanoCAGE zebrafish TU testis rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_testis_BR1.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR1.R2.fastq.gz fastq fastq 2655464100.0 17518322.0 nano TUzfish combined deep testis BR1.R1.fastq.gz 0:75.79 1:75.79 A:648423774;C:624425183;G:667510545;T:714557704;N:546894 75 75     648423774 624425183 667510545 714557704 546894 SRX14464503 SRS11744582 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.05205 0.9337 0.00433 0.0458 0.92086 0.68631 0.5426 0.50321 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Gonad Reproductive System
68256 68256 SRR18327320 SRX14464502 SRS11744580 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow nanoCAGE zebrafish TU brain rep2 nanoCAGE zebrafish TU brain rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_brain_BR2.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR2.R2.fastq.gz fastq fastq 2120070300.0 13983927.0 nano TUzfish combined deep brain BR2.R1.fastq.gz 0:75.80 1:75.80 A:521597394;C:502052046;G:539140115;T:556851976;N:428769 75 75     521597394 502052046 539140115 556851976 428769 SRX14464502 SRS11744580 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.05946 0.93361 0.00648 0.07284 0.91739 0.70025 0.57506 0.48669 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Brain Nervous System
68257 68257 SRR18327321 SRX14464501 SRS11744579 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow nanoCAGE zebrafish TU brain rep1 nanoCAGE zebrafish TU brain rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_brain_BR1.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR1.R2.fastq.gz fastq fastq 1958802000.0 12919047.0 nano TUzfish combined deep brain BR1.R1.fastq.gz 0:75.81 1:75.81 A:485271176;C:461368873;G:496521163;T:515247447;N:393341 75 75     485271176 461368873 496521163 515247447 393341 SRX14464501 SRS11744579 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.0666 0.93487 0.00689 0.0747 0.91175 0.70027 0.57062 0.49364 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Brain Nervous System
68258 68258 SRR17709722 SRX13872770 SRS11744581 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis nanoCAGE zebrafish TU testis rep2 nanoCAGE zebrafish TU testis shallow rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_testis_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep2.R2.fastq.gz fastq fastq 1257997200.0 8218216.0 nanoCAGE zebrafish TU testis rep2.R1.fastq.gz 0:76.54 1:76.54 A:307675653;C:294445668;G:315944501;T:339570175;N:361203 76 76     307675653 294445668 315944501 339570175 361203 SRX13872770 SRS11744581 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.06846 0.93772 0.00675 0.04699 0.90293 0.67986 0.52867 0.49221 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Gonad Reproductive System
68259 68259 SRR17709723 SRX13872769 SRS11744582 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis nanoCAGE zebrafish TU testis rep1 nanoCAGE zebrafish TU testis shallow rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_testis_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep1.R2.fastq.gz fastq fastq 1351312800.0 8823980.0 nanoCAGE zebrafish TU testis rep1.R1.fastq.gz 0:76.57 1:76.57 A:329750139;C:318355694;G:339653380;T:363149300;N:404287 76 76     329750139 318355694 339653380 363149300 404287 SRX13872769 SRS11744582 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.06051 0.93247 0.00473 0.0437 0.91088 0.68943 0.52768 0.49868 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Gonad Reproductive System
68260 68260 SRR17709724 SRX13872768 SRS11744580 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult female brain nanoCAGE zebrafish TU brain rep2 nanoCAGE zebrafish TU brain shallow rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_brain_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep2.R2.fastq.gz fastq fastq 1114647450.0 7281108.0 nanoCAGE zebrafish TU brain rep2.R1.fastq.gz 0:76.54 1:76.54 A:273967636;C:264512491;G:283567362;T:292276557;N:323404 76 76     273967636 264512491 283567362 292276557 323404 SRX13872768 SRS11744580 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.06736 0.93327 0.00663 0.0712 0.90792 0.70283 0.55337 0.4859 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Brain Nervous System
68261 68261 SRR17709725 SRX13872767 SRS11744579 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult female brain nanoCAGE zebrafish TU brain rep1 nanoCAGE zebrafish TU brain shallow rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_brain_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep1.R2.fastq.gz fastq fastq 1040194800.0 6794999.0 nanoCAGE zebrafish TU brain rep1.R1.fastq.gz 0:76.54 1:76.54 A:257427323;C:245563114;G:263853643;T:273054571;N:296149 76 76     257427323 245563114 263853643 273054571 296149 SRX13872767 SRS11744579 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.07308 0.93461 0.00714 0.07167 0.9051 0.70199 0.56162 0.48821 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;