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28 rows where devstage_curation = "Blastula" and experiment.library_selection = "CAGE"

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tissue_curation 3

tissue_curation_coarse 2

experiment.library_strategy 2

experiment.library_layout 2

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • CAGE · 28 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Blastula · 28 ✖
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
36416 36416 SRR516554 SRX156349 SRS347209 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo dome/zfs:0000015 stage D. rerio dome/zfs:0000015 embryo D. rerio dome/zfs:0000015 embryo                     CAGE D. rerio dome/zfs:0000015 embryo CAGE D. rerio dome/zfs:0000015 embryo D. rerio dome/zfs:0000015 embryo 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</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> SRP013950     CAGE_30p_dome.fastq fastq 165690819.0 6136697.0 CAGE D. rerio dome/zfs:0000015 embryo 0:27 A:42721293;C:36492232;G:46154926;T:40322368;N:0 27       42721293 36492232 46154926 40322368 0 SRX156349 SRS347209 SRA055273 University of Bergen ZEPROME consortium 1 0.50236   0.0905   0.81824   0.8156   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Blastula Embryo Embryo Imprecise All anatomical structures
36417 36417 SRR516552 SRX156347 SRS347208 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo sphere/dome stage D. rerio sphere/dome embryo D. rerio sphere/dome embryo                     CAGE D. rerio sphere/dome embryo CAGE D. rerio sphere/dome embryo run2 D. rerio sphere/dome embryo 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</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> SRP013950     CAGE_sphere_dome_run1.fastq fastq 78937740.0 2923620.0 CAGE D. rerio sphere/dome embryo run1 0:27 A:20705496;C:17020957;G:22237043;T:18974244;N:0 27       20705496 17020957 22237043 18974244 0 SRX156347 SRS347208 SRA055273 University of Bergen ZEPROME consortium 1 0.50917   0.09193   0.81523   0.8084   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Blastula Embryo Embryo Imprecise All anatomical structures
36418 36418 SRR516553 SRX156347 SRS347208 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo sphere/dome stage D. rerio sphere/dome embryo D. rerio sphere/dome embryo                     CAGE D. rerio sphere/dome embryo CAGE D. rerio sphere/dome embryo run2 D. rerio sphere/dome embryo 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</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> SRP013950     CAGE_sphere_dome_run2.fastq fastq 82071009.0 3039667.0 CAGE D. rerio sphere/dome embryo run2 0:27 A:20823133;C:17914934;G:22973465;T:20359477;N:0 27       20823133 17914934 22973465 20359477 0 SRX156347 SRS347208 SRA055273 University of Bergen ZEPROME consortium 1 0.47213   0.07583   0.82384   0.8313   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Blastula Embryo Embryo Imprecise All anatomical structures
36419 36419 SRR516551 SRX156338 SRS347207 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo oblong stage D. rerio oblong embryo D. rerio oblong embryo                     CAGE D. rerio oblong embryo CAGE D. rerio oblong embryo D. rerio oblong embryo 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</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> SRP013950         135892080.0 5033040.0 CAGE D. rerio oblong embryo 0:27 A:34565898;C:30442218;G:38967845;T:31916119;N:0 27       34565898 30442218 38967845 31916119 0 SRX156338 SRS347207 SRA055273 University of Bergen ZEPROME consortium 1 0.56265   0.09335   0.80068   0.70759   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Blastula Embryo Embryo Imprecise All anatomical structures
36421 36421 SRR516549 SRX156336 SRS347204 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo 512 cells stage D. rerio 512 cells embryo D. rerio 512 cells embyo                     CAGE D. rerio 512 cells embryo CAGE D. rerio 512 cells embryo D. rerio 512 cells embryo 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</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> SRP013950     CAGE_512cells.fastq fastq 150228810.0 5564030.0 CAGE D. rerio 512 cells embryo 0:27 A:37826960;C:33838922;G:43403014;T:35159914;N:0 27       37826960 33838922 43403014 35159914 0 SRX156336 SRS347204 SRA055273 University of Bergen ZEPROME consortium 1 0.57925   0.08753   0.79933   0.72579   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Blastula Embryo Embryo Imprecise All anatomical structures
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
55272 55272 SRR10215488 SRX6935167 SRS5465202 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         S04 30Epi   strain:AB|dev stage:zfs:0000015|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo zfs:0000015 stage zfs:0000015 nAnTiCAGE zfs:0000015 nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP223930     S04_30pEpib_nAnTiCAGE.fastq.gz fastq 629440272.0 13113339.0 S04 30pEpib nAnTiCAGE.fastq.gz 0:48 1:0 A:170201862;C:150343558;G:166046900;T:141987430;N:860522 48 0     170201862 150343558 166046900 141987430 860522 SRX6935167 SRS5465202 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 1 0.83843   0.15935   0.81499   0.71304   48   B   usable mapping rate illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Blastula Embryo Whole Organism All anatomical structures
55273 55273 SRR10215489 SRX6935166 SRS5465201 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         S03 512Cells   strain:AB|dev stage:512 cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo 512 cell stage 512Cells nAnTiCAGE 512Cells nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP223930     S03_512Cells_nAnTiCAGE.fastq.gz fastq 725783040.0 15120480.0 S03 512Cells nAnTiCAGE.fastq.gz 0:48 1:0 A:196224130;C:171017037;G:189882541;T:167660445;N:998887 48 0     196224130 171017037 189882541 167660445 998887 SRX6935166 SRS5465201 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 1 0.85441   0.14832   0.79659   0.68016   48   B   usable mapping rate illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Blastula Embryo Whole Organism All anatomical structures
55274 55274 SRR10215490 SRX6935165 SRS5465200 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         S02 128Cells   strain:AB|dev stage:128 cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo 128 cell stage 128Cells nAnTiCAGE 128Cells nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP223930     S02_128Cells_nAnTiCAGE.fastq.gz fastq 510549408.0 10636446.0 S02 128Cells nAnTiCAGE.fastq.gz 0:48 1:0 A:135389960;C:121538362;G:140642547;T:112273195;N:705344 48 0     135389960 121538362 140642547 112273195 705344 SRX6935165 SRS5465200 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 1 0.84843   0.14523   0.79845   0.68592   48   B   usable mapping rate illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Blastula Embryo Whole Organism All anatomical structures
69378 69378 SRR18516702 SRX14647801 SRS12413210 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007475BS   strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq zfs:0000015 Whole cell CAGE DCD003740SQ DCD003740SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003740SQ.USERdanio-user.R1.fastq.gz fastq 57981552.0 1207949.0 CAGE seq Mueller lab 0013AS.DCD003740SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:13228227;C:15492921;G:15505739;T:13750626;N:4039 48 0     13228227 15492921 15505739 13750626 4039 SRX14647801 SRS12413210 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.18388   0.02619   0.85811   0.52264   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Blastula Embryo Embryo Imprecise All anatomical structures
69389 69389 SRR18516713 SRX14647790 SRS12413209 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007478BS   strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq zfs:0000015 Nuclear CAGE DCD003732SQ DCD003732SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003732SQ.USERdanio-user.R1.fastq.gz fastq 833831760.0 17371495.0 CAGE seq Mueller lab 0014AS.DCD003732SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:184529953;C:221676233;G:220734592;T:206820467;N:70515 48 0     184529953 221676233 220734592 206820467 70515 SRX14647790 SRS12413209 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.16336   0.03655   0.88633   0.47894   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Blastula Embryo Embryo Imprecise All anatomical structures
69398 69398 SRR18516722 SRX14647781 SRS12413210 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007475BS   strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq zfs:0000015 Whole cell CAGE DCD003720SQ DCD003720SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003720SQ.USERdanio-user.R1.fastq.gz fastq 536292432.0 11172759.0 CAGE seq Mueller lab 0013AS.DCD003720SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:122756671;C:142850582;G:140364671;T:130293257;N:27251 48 0     122756671 142850582 140364671 130293257 27251 SRX14647781 SRS12413210 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.23072   0.04674   0.89572   0.59187   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Blastula Embryo Embryo Imprecise All anatomical structures
69399 69399 SRR18516723 SRX14647780 SRS12413210 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007475BS   strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq zfs:0000015 Whole cell CAGE DCD003725SQ DCD003725SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003725SQ.USERdanio-user.R1.fastq.gz fastq 1839979776.0 38332912.0 CAGE seq Mueller lab 0013AS.DCD003725SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:422772310;C:484519947;G:479159876;T:453437875;N:89768 48 0     422772310 484519947 479159876 453437875 89768 SRX14647780 SRS12413210 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.22646   0.03978   0.88574   0.556   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Blastula Embryo Embryo Imprecise All anatomical structures
69400 69400 SRR18516724 SRX14647779 SRS12413209 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007478BS   strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq zfs:0000015 Nuclear CAGE DCD003728SQ DCD003728SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003728SQ.USERdanio-user.R1.fastq.gz fastq 778510272.0 16218964.0 CAGE seq Mueller lab 0014AS.DCD003728SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:170505572;C:207531743;G:206655879;T:193751108;N:65970 48 0     170505572 207531743 206655879 193751108 65970 SRX14647779 SRS12413209 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.1419   0.02783   0.8954   0.49693   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Blastula Embryo Embryo Imprecise All anatomical structures
69401 69401 SRR18516725 SRX14647778 SRS12413209 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007478BS   strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq zfs:0000015 Nuclear CAGE DCD003724SQ DCD003724SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003724SQ.USERdanio-user.R1.fastq.gz fastq 641108496.0 13356427.0 CAGE seq Mueller lab 0014AS.DCD003724SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:143927298;C:167543966;G:171107575;T:158473503;N:56154 48 0     143927298 167543966 171107575 158473503 56154 SRX14647778 SRS12413209 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.20203   0.0454   0.87091   0.51364   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Blastula Embryo Embryo Imprecise All anatomical structures

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