{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"CAGE\" and experiment.library_strategy = \"OTHER\"", "rows": [[9803, "ERR3909553", "ERX3918377", "ERS4309135", "ERP120006", "PRJEB36776", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast   green vs slow   red", "E-MTAB-8795", "Transcriptome Analysis", "The core promoter  a stretch of DNA surrounding the transcription start site TSS  is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol  1543  57 109.", "Total1", "SAMEA6544758", "UNIVERSITY OF BIRMINGHAM", "ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544758|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast   green vs slow   red", "E MTAB 8795:Total1 s", "Total1 s", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast   green vs slow   red", "Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol  1543  57 109.", "Red3", "SAMEA6544757", "UNIVERSITY OF BIRMINGHAM", "ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544757|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast   green vs slow   red", "E MTAB 8795:Red3 s", "Red3 s", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast   green vs slow   red", "Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in:  Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  Morlighem  J.E.  Suzuki  M.  Plessy  C. and Harbers  M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  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Cellular differentiation is marked by divergence in transcriptional repertoire and cell  cycling behaviour between cells of different fates. The role promoter associated gene  regulatory networks play in development associated transitions in cell cycle  dynamics is poorly understood. This study demonstrates in a vertebrate embryo  how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development  using the FUCCI transgenic cell cycle  phase marker  revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process  cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer  PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma  for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100  Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain  S.  Kato  S.  Arnaud  O.  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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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo oblong stage", "D. rerio oblong embryo", "D. rerio oblong embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio oblong embryo", "CAGE   D. rerio oblong embryo", "D. rerio oblong embryo", "1", null, null, "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", null, null, null, null, 135892080.0, 5033040.0, "CAGE   D. rerio oblong embryo", "0:27", "A:34565898;C:30442218;G:38967845;T:31916119;N:0", 27, null, null, null, 34565898, 30442218, 38967845, 31916119, 0, "SRX156338", "SRS347207", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.56265, null, 0.09335, null, 0.80068, null, 0.70759, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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. 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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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo high stage", "D. rerio high embryo", "D. rerio high embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio high embryo", "CAGE   D. rerio high embryo", "D. rerio high embryo", "1", null, null, "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", null, null, "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, null, null, null, 33693838, 27629256, 36692263, 30577489, 0, "SRX156337", "SRS347206", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.53282, null, 0.08323, null, 0.80854, null, 0.77395, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2013-08-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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. 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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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 512 cells stage", "D. rerio 512 cells embryo", "D. rerio 512 cells embyo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 512 cells embryo", "CAGE   D. rerio 512 cells embryo", "D. rerio 512 cells embryo", "1", null, null, "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", null, null, "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, null, null, null, 37826960, 33838922, 43403014, 35159914, 0, "SRX156336", "SRS347204", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.57925, null, 0.08753, null, 0.79933, null, 0.72579, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 64 cells stage", "D. rerio 64 cells embryo", "D. rerio 64 cells embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 64 cells embryo", "CAGE   D. rerio 64 cells embryo", "D. rerio 64 cells embryo", "1", null, null, "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", null, null, "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, null, null, null, 41192860, 36547869, 46848833, 38194626, 0, "SRX156334", "SRS347202", "SRA055273", "University of Bergen", "ZEPROME consortium", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2013-08-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36423, "SRR516547", "SRX156325", "SRS347201", "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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   fertilized egg", "D. rerio fertilized egg", "D. rerio fertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio fertilized egg", "CAGE   D. rerio fertilized egg", "D. rerio fertilized egg", "1", null, null, "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", null, null, "CAGE_fertilized_egg.fastq", "fastq", 160948350.0, 5961050.0, "CAGE   D. rerio fertilized egg", "0:27", "A:42030009;C:34700589;G:45399755;T:38817997;N:0", 27, null, null, null, 42030009, 34700589, 45399755, 38817997, 0, "SRX156325", "SRS347201", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.49394, null, 0.07554, null, 0.81684, null, 0.79759, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [36424, "SRR516545", "SRX156307", "SRS347187", "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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   unfertilized egg", "D. rerio unfertilized egg", "D. rerio unfertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio unfertilized egg", "CAGE   D. rerio unfertilized egg run2", "D. rerio unfertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 115273233.0, 4269379.0, "CAGE   D. rerio unfertilized egg run1", "0:27", "A:29909511;C:24823784;G:32519899;T:28020039;N:0", 27, null, null, null, 29909511, 24823784, 32519899, 28020039, 0, "SRX156307", "SRS347187", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.49872, null, 0.07655, null, 0.81673, null, 0.80445, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [36425, "SRR516546", "SRX156307", "SRS347187", "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.", null, "pubmed:24531765", "Zebrafish wild type AB strain   unfertilized egg", "D. rerio unfertilized egg", "D. rerio unfertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio unfertilized egg", "CAGE   D. rerio unfertilized egg run2", "D. rerio unfertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 112673943.0, 4173109.0, "CAGE   D. rerio unfertilized egg run2", "0:27", "A:28315221;C:24199098;G:32599482;T:27560142;N:0", 27, null, null, null, 28315221, 24199098, 32599482, 27560142, 0, "SRX156307", "SRS347187", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.46201, null, 0.06422, null, 0.82118, null, 0.82184, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL7F transgenic line", null, "strain:AB strain MUTL7F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL7F transgenic line", null, "strain:AB strain MUTL7F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2", "D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2", "1", "1", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL6F transgenic line", null, "strain:AB strain MUTL6F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL6F transgenic line", null, "strain:AB strain MUTL6F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2", "D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2", "1", "1", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL5F transgenic line", null, "strain:AB strain MUTL5F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL5F transgenic line", null, "strain:AB strain MUTL5F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2", "D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2", "1", "1", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL2F transgenic line", null, "strain:AB strain MUTL2F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:24531765", "stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry", "Generic sample from Danio rerio", "D. rerio MUTL2F transgenic line", null, "strain:AB strain MUTL2F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2", "D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2", "1", "1", null, null, "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", null, null, "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, null, null, 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", null, "Unknown", "2014-02-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "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", null, "strain:AB strain WTL3F line|development stage:high 3.3 hpf", null, null, null, null, null, null, null, null, "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", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", 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