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38 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "CAGE" and tissue_curation = "Embryo Imprecise"

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devstage_curation 6

experiment.library_strategy 2

tissue_curation_coarse 1

tissue_curation 1

  • Embryo Imprecise · 38 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • CAGE · 38 ✖

experiment.library_layout 1

  • SINGLE · 38 ✖

devstage_curation_coarse 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
36409 36409 SRR516560 SRX156356 SRS347213 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 prim20 stage D. rerio prim20 embryo D. rerio prim20 embryo                     CAGE D. rerio prim20 embryo CAGE D. rerio prim20 embryo run2 D. rerio prim20 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_prim20_run1.fastq fastq 76770666.0 2843358.0 CAGE D. rerio prim20 embryo run1 0:27 A:19320047;C:17585086;G:22511175;T:17354358;N:0 27       19320047 17585086 22511175 17354358 0 SRX156356 SRS347213 SRA055273 University of Bergen ZEPROME consortium 1 0.56472   0.10044   0.77469   0.74192   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Undetermined Embryo Embryo Imprecise All anatomical structures
36410 36410 SRR516561 SRX156356 SRS347213 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 prim20 stage D. rerio prim20 embryo D. rerio prim20 embryo                     CAGE D. rerio prim20 embryo CAGE D. rerio prim20 embryo run2 D. rerio prim20 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_prim20_run2.fastq fastq 163254906.0 6046478.0 CAGE D. rerio prim20 embryo run2 0:27 A:40211042;C:36959797;G:46866669;T:39217398;N:0 27       40211042 36959797 46866669 39217398 0 SRX156356 SRS347213 SRA055273 University of Bergen ZEPROME consortium 1 0.47475   0.06947   0.78409   0.78014   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2013-08-31 Undetermined Embryo Embryo Imprecise All anatomical structures
36411 36411 SRR516559 SRX156355 SRS347212 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 prim6 stage D. rerio prim6 embryo D. rerio prim6 embryo                     CAGE D. rerio prim6 embryo CAGE D. rerio prim6 embryo D. rerio prim6 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_prim6.fastq fastq 283414275.0 10496825.0 CAGE D. rerio prim6 embryo 0:27 A:70974303;C:66202040;G:80064124;T:66173808;N:0 27       70974303 66202040 80064124 66173808 0 SRX156355 SRS347212 SRA055273 University of Bergen ZEPROME consortium 1 0.53395   0.07806   0.78255   0.77575   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2013-08-31 Undetermined Embryo Embryo Imprecise All anatomical structures
36412 36412 SRR516557 SRX156352 SRS347211 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 14 somites stage D. rerio 14 somites embryo D. rerio 14 somites embryo                     CAGE D. rerio 14 somites embryo CAGE D. rerio 14 somites embryo run2 D. rerio 14 somites 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         73689048.0 2729224.0 CAGE D. rerio 14 somites embryo run1 0:27 A:19506796;C:16238588;G:21636330;T:16307334;N:0 27       19506796 16238588 21636330 16307334 0 SRX156352 SRS347211 SRA055273 University of Bergen ZEPROME consortium 1 0.63348   0.09461   0.76199   0.68697   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Segmentation Embryo Embryo Imprecise All anatomical structures
36413 36413 SRR516558 SRX156352 SRS347211 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 14 somites stage D. rerio 14 somites embryo D. rerio 14 somites embryo                     CAGE D. rerio 14 somites embryo CAGE D. rerio 14 somites embryo run2 D. rerio 14 somites 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_14somites_run2.fastq fastq 212381811.0 7865993.0 CAGE D. rerio 14 somites embryo run2 0:27 A:53780820;C:47467464;G:59893810;T:51239717;N:0 27       53780820 47467464 59893810 51239717 0 SRX156352 SRS347211 SRA055273 University of Bergen ZEPROME consortium 1 0.5278   0.0806   0.77589   0.72881   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Segmentation Embryo Embryo Imprecise All anatomical structures
36414 36414 SRR516555 SRX156350 SRS347210 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 shield stage D. rerio shield embryo D. rerio shield embryo                     CAGE D. rerio shield embryo CAGE D. rerio shield embryo run2 D. rerio shield 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         81086886.0 3003218.0 CAGE D. rerio shield embryo run1 0:27 A:20800196;C:18582826;G:23491216;T:18212648;N:0 27       20800196 18582826 23491216 18212648 0 SRX156350 SRS347210 SRA055273 University of Bergen ZEPROME consortium 1 0.60434   0.09948   0.80432   0.72631   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Gastrula Embryo Embryo Imprecise All anatomical structures
36415 36415 SRR516556 SRX156350 SRS347210 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 shield stage D. rerio shield embryo D. rerio shield embryo                     CAGE D. rerio shield embryo CAGE D. rerio shield embryo run2 D. rerio shield 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_shield_run2.fastq fastq 81675891.0 3025033.0 CAGE D. rerio shield embryo run2 0:27 A:21590166;C:17662459;G:22692127;T:19731139;N:0 27       21590166 17662459 22692127 19731139 0 SRX156350 SRS347210 SRA055273 University of Bergen ZEPROME consortium 1 0.52624   0.08062   0.81793   0.76291   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Gastrula Embryo Embryo Imprecise All anatomical structures
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
36420 36420 SRR516550 SRX156337 SRS347206 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 high stage D. rerio high embryo D. rerio high embryo                     CAGE D. rerio high embryo CAGE D. rerio high embryo D. rerio high 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_high.fastq fastq 128592846.0 4762698.0 CAGE D. rerio high embryo 0:27 A:33693838;C:27629256;G:36692263;T:30577489;N:0 27       33693838 27629256 36692263 30577489 0 SRX156337 SRS347206 SRA055273 University of Bergen ZEPROME consortium 1 0.53282   0.08323   0.80854   0.77395   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2013-08-31 Undetermined 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
36422 36422 SRR516548 SRX156334 SRS347202 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 64 cells stage D. rerio 64 cells embryo D. rerio 64 cells embryo                     CAGE D. rerio 64 cells embryo CAGE D. rerio 64 cells embryo D. rerio 64 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_64cells.fastq fastq 162784188.0 6029044.0 CAGE D. rerio 64 cells embryo 0:27 A:41192860;C:36547869;G:46848833;T:38194626;N:0 27       41192860 36547869 46848833 38194626 0 SRX156334 SRS347202 SRA055273 University of Bergen ZEPROME consortium                       B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2013-08-31 Cleavage Embryo Embryo Imprecise 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
69379 69379 SRR18516703 SRX14647800 SRS12413216 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007476BS   strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq Prim Nuclear CAGE DCD003719SQ DCD003719SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003719SQ.USERdanio-user.R1.fastq.gz fastq 585510192.0 12198129.0 CAGE seq Mueller lab 0014AS.DCD003719SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:129885703;C:153766182;G:160138903;T:141666883;N:52521 48 0     129885703 153766182 160138903 141666883 52521 SRX14647800 SRS12413216 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.20391   0.04196   0.83453   0.4979   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69380 69380 SRR18516704 SRX14647799 SRS12413216 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007476BS   strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq Prim Nuclear CAGE DCD003718SQ DCD003718SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003718SQ.USERdanio-user.R1.fastq.gz fastq 593136528.0 12357011.0 CAGE seq Mueller lab 0014AS.DCD003718SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:130366174;C:156810351;G:159219365;T:146691922;N:48716 48 0     130366174 156810351 159219365 146691922 48716 SRX14647799 SRS12413216 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.14873   0.03239   0.86557   0.49634   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69381 69381 SRR18516705 SRX14647798 SRS12413216 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007476BS   strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq Prim Nuclear CAGE DCD003723SQ DCD003723SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003723SQ.USERdanio-user.R1.fastq.gz fastq 422696256.0 8806172.0 CAGE seq Mueller lab 0014AS.DCD003723SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:92712632;C:111696999;G:115145846;T:103105611;N:35168 48 0     92712632 111696999 115145846 103105611 35168 SRX14647798 SRS12413216 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.1594   0.02997   0.85591   0.48496   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69382 69382 SRR18516706 SRX14647797 SRS12413215 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007477BS   strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq High pec Nuclear CAGE DCD003737SQ DCD003737SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003737SQ.USERdanio-user.R1.fastq.gz fastq 1041108672.0 21689764.0 CAGE seq Mueller lab 0014AS.DCD003737SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:233996885;C:276232291;G:275987771;T:254800016;N:91709 48 0     233996885 276232291 275987771 254800016 91709 SRX14647797 SRS12413215 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.19665   0.0423   0.84271   0.49525   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69383 69383 SRR18516707 SRX14647796 SRS12413215 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007477BS   strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq High pec Nuclear CAGE DCD003729SQ DCD003729SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003729SQ.USERdanio-user.R1.fastq.gz fastq 383268528.0 7984761.0 CAGE seq Mueller lab 0014AS.DCD003729SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:83789437;C:103371728;G:102876480;T:93198236;N:32647 48 0     83789437 103371728 102876480 93198236 32647 SRX14647796 SRS12413215 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.15605   0.03059   0.86951   0.50369   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69384 69384 SRR18516708 SRX14647795 SRS12413215 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007477BS   strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq High pec Nuclear CAGE DCD003734SQ DCD003734SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003734SQ.USERdanio-user.R1.fastq.gz fastq 560665392.0 11680529.0 CAGE seq Mueller lab 0014AS.DCD003734SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:123278501;C:149059346;G:152514412;T:135763704;N:49429 48 0     123278501 149059346 152514412 135763704 49429 SRX14647795 SRS12413215 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.16518   0.02906   0.85283   0.47924   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69385 69385 SRR18516709 SRX14647794 SRS12413214 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007471BS   strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq High pec Whole cell CAGE DCD003731SQ DCD003731SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003731SQ.USERdanio-user.R1.fastq.gz fastq 534745104.0 11140523.0 CAGE seq Mueller lab 0013AS.DCD003731SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:122900964;C:145291239;G:142314928;T:124199394;N:38579 48 0     122900964 145291239 142314928 124199394 38579 SRX14647794 SRS12413214 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.21193   0.03662   0.8576   0.51061   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69386 69386 SRR18516710 SRX14647793 SRS12413214 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007471BS   strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq High pec Whole cell CAGE DCD003733SQ DCD003733SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003733SQ.USERdanio-user.R1.fastq.gz fastq 1106623152.0 23054649.0 CAGE seq Mueller lab 0013AS.DCD003733SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:244437769;C:302018709;G:293780395;T:266329857;N:56422 48 0     244437769 302018709 293780395 266329857 56422 SRX14647793 SRS12413214 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.25973   0.02959   0.84778   0.50948   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69387 69387 SRR18516711 SRX14647792 SRS12413214 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007471BS   strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq High pec Whole cell CAGE DCD003735SQ DCD003735SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003735SQ.USERdanio-user.R1.fastq.gz fastq 829987920.0 17291415.0 CAGE seq Mueller lab 0013AS.DCD003735SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:189638839;C:226118233;G:218991435;T:195178858;N:60555 48 0     189638839 226118233 218991435 195178858 60555 SRX14647792 SRS12413214 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.20953   0.03562   0.85285   0.52927   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69388 69388 SRR18516712 SRX14647791 SRS12413213 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007472BS   strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq 5 9 somites Whole cell CAGE DCD003730SQ DCD003730SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003730SQ.USERdanio-user.R1.fastq.gz fastq 358730736.0 7473557.0 CAGE seq Mueller lab 0013AS.DCD003730SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:82114871;C:96481695;G:97889447;T:82217691;N:27032 48 0     82114871 96481695 97889447 82217691 27032 SRX14647791 SRS12413213 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.22955   0.03488   0.84719   0.51204   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Segmentation 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
69390 69390 SRR18516714 SRX14647789 SRS12413213 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007472BS   strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq 5 9 somites Whole cell CAGE DCD003738SQ DCD003738SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003738SQ.USERdanio-user.R1.fastq.gz fastq 1160622288.0 24179631.0 CAGE seq Mueller lab 0013AS.DCD003738SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:261568282;C:313737609;G:310169539;T:275088632;N:58226 48 0     261568282 313737609 310169539 275088632 58226 SRX14647789 SRS12413213 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.27025   0.0344   0.86505   0.50961   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Segmentation Embryo Embryo Imprecise All anatomical structures
69391 69391 SRR18516715 SRX14647788 SRS12413213 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007472BS   strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq 5 9 somites Whole cell CAGE DCD003722SQ DCD003722SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003722SQ.USERdanio-user.R1.fastq.gz fastq 666656256.0 13888672.0 CAGE seq Mueller lab 0013AS.DCD003722SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:149770159;C:178068662;G:177661463;T:161122864;N:33108 48 0     149770159 178068662 177661463 161122864 33108 SRX14647788 SRS12413213 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.25511   0.02671   0.86436   0.50531   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Segmentation Embryo Embryo Imprecise All anatomical structures
69392 69392 SRR18516716 SRX14647787 SRS12413212 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007473BS   strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq Prim Whole cell CAGE DCD003727SQ DCD003727SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003727SQ.USERdanio-user.R1.fastq.gz fastq 924879888.0 19268331.0 CAGE seq Mueller lab 0013AS.DCD003727SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:214005056;C:251321459;G:244648845;T:214835794;N:68734 48 0     214005056 251321459 244648845 214835794 68734 SRX14647787 SRS12413212 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.2165   0.03701   0.84768   0.54102   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69393 69393 SRR18516717 SRX14647786 SRS12413212 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007473BS   strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq Prim Whole cell CAGE DCD003717SQ DCD003717SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003717SQ.USERdanio-user.R1.fastq.gz fastq 1485845376.0 30955112.0 CAGE seq Mueller lab 0013AS.DCD003717SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:329122121;C:402514173;G:390388645;T:363745867;N:74570 48 0     329122121 402514173 390388645 363745867 74570 SRX14647786 SRS12413212 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.23893   0.0248   0.86125   0.50849   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69394 69394 SRR18516718 SRX14647785 SRS12413212 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007473BS   strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:2|BioSampleModel:Model organism or animal                 CAGE seq Prim Whole cell CAGE DCD003739SQ DCD003739SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0013AS.DCD003739SQ.USERdanio-user.R1.fastq.gz fastq 1372622736.0 28596307.0 CAGE seq Mueller lab 0013AS.DCD003739SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:306709302;C:373224967;G:360990874;T:331626639;N:70954 48 0     306709302 373224967 360990874 331626639 70954 SRX14647785 SRS12413212 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.26574   0.02914   0.85113   0.52147   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
69395 69395 SRR18516719 SRX14647784 SRS12413211 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007474BS   strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq 5 9 somites Nuclear CAGE DCD003721SQ DCD003721SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003721SQ.USERdanio-user.R1.fastq.gz fastq 425483904.0 8864248.0 CAGE seq Mueller lab 0014AS.DCD003721SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:98642418;C:114264552;G:114112965;T:98433833;N:30136 48 0     98642418 114264552 114112965 98433833 30136 SRX14647784 SRS12413211 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.21658   0.03797   0.85226   0.48604   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Segmentation Embryo Embryo Imprecise All anatomical structures
69396 69396 SRR18516720 SRX14647783 SRS12413211 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007474BS   strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq 5 9 somites Nuclear CAGE DCD003736SQ DCD003736SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003736SQ.USERdanio-user.R1.fastq.gz fastq 533681088.0 11118356.0 CAGE seq Mueller lab 0014AS.DCD003736SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:115850766;C:142773032;G:143794343;T:131220159;N:42788 48 0     115850766 142773032 143794343 131220159 42788 SRX14647783 SRS12413211 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.15054   0.0279   0.87434   0.4867   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Segmentation Embryo Embryo Imprecise All anatomical structures
69397 69397 SRR18516721 SRX14647782 SRS12413211 SRP366491 PRJNA821088 Enhancer calling in early stages PRJNA821088 Other CAGE seq for enhancer calling in early stages for the DANIO CODE project.         DCD007474BS   strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab University of Birmingham|replicate:1|BioSampleModel:Model organism or animal                 CAGE seq 5 9 somites Nuclear CAGE DCD003726SQ DCD003726SQ max read length:50     RNA-Seq TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   SRP366491     CAGE-seq_Mueller_lab_0014AS.DCD003726SQ.USERdanio-user.R1.fastq.gz fastq 250307520.0 5214740.0 CAGE seq Mueller lab 0014AS.DCD003726SQ.USERdanio user.R1.fastq.gz 0:48 1:0 A:55705158;C:65429159;G:68119770;T:61031856;N:21577 48 0     55705158 65429159 68119770 61031856 21577 SRX14647782 SRS12413211 SRA1393740 DANIO-CODE|Department for Biosciences and Nutrition DANIO-CODE DANIO-CODE 1 0.19864   0.04157   0.85279   0.48786   48   B   usable mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2022-03-29 Segmentation 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");;