{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.platform = \"ABI_SOLID\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[36255, "SRR062662", "SRX025030", "SRS085809", "SRP003165", "PRJNA127881", "High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line", "GSE22830", "Transcriptome Analysis", "mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "5.3hpf", "GSM564432", null, "tissue:developing embryos|background:AB; wild type|developmental stage:post MBT stage embryo 5.3hpf", "5.3hpf", "ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.", "developing embryos", "Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.", "mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.", "Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.", "background:AB; wild type|developmental stage:post MBT stage embryo 5.3hpf", "GSM564432", "GSM564432: 5.3hpf", "GSM564432: 5.3hpf", "GSM564432: 5.3hpf", "1", null, "GEO Accession:GSM564432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>", "SRP003165", null, null, null, null, 2778008350.0, 55560167.0, "GSM564432 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025030", "SRS085809", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.7379, null, 0.09683, null, 0.84751, null, 0.5252, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36256, "SRR062661", "SRX025029", "SRS085808", "SRP003165", "PRJNA127881", "High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line", "GSE22830", "Transcriptome Analysis", "mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "3.5hpf", "GSM564431", null, "tissue:developing embryos|background:AB; wild type|developmental stage:MBT stage embryo 3.5hpf", "3.5hpf", "ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.", "developing embryos", "Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.", "mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.", "Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.", "background:AB; wild type|developmental stage:MBT stage embryo 3.5hpf", "GSM564431", "GSM564431: 3.5hpf", "GSM564431: 3.5hpf", "GSM564431: 3.5hpf", "1", null, "GEO Accession:GSM564431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>", "SRP003165", null, null, null, null, 1894338450.0, 37886769.0, "GSM564431 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025029", "SRS085808", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.73958, null, 0.04864, null, 0.82378, null, 0.49728, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36257, "SRR062660", "SRX025028", "SRS085807", "SRP003165", "PRJNA127881", "High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line", "GSE22830", "Transcriptome Analysis", "mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "128/256 cells", "GSM564430", null, "tissue:developing embryos|background:AB; wild type|developmental stage:mixure of 128/256 cell embryos", "128/256 cells", "ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.", "developing embryos", "Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.", "mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.", "Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.", "background:AB; wild type|developmental stage:mixure of 128/256 cell embryos", "GSM564430", "GSM564430: 128/256 cells", "GSM564430: 128/256 cells", "GSM564430: 128/256 cells", "1", null, "GEO Accession:GSM564430", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>", "SRP003165", null, null, null, null, 1355951300.0, 27119026.0, "GSM564430 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025028", "SRS085807", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.73373, null, 0.03657, null, 0.82773, null, 0.50091, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36258, "SRR062659", "SRX025027", "SRS085806", "SRP003165", "PRJNA127881", "High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line", "GSE22830", "Transcriptome Analysis", "mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "16/32 cells", "GSM564429", null, "tissue:developing embryos|background:AB; wild type|developmental stage:mixure of 16/32 cell embryos", "16/32 cells", "ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.", "developing embryos", "Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.", "mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.", "Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.", "background:AB; wild type|developmental stage:mixure of 16/32 cell embryos", "GSM564429", "GSM564429: 16/32 cells", "GSM564429: 16/32 cells", "GSM564429: 16/32 cells", "1", null, "GEO Accession:GSM564429", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>", "SRP003165", null, null, null, null, 1792238300.0, 35844766.0, "GSM564429 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025027", "SRS085806", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.6993, null, 0.04019, null, 0.83763, null, 0.50284, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36259, "SRR062658", "SRX025026", "SRS085805", "SRP003165", "PRJNA127881", "High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line", "GSE22830", "Transcriptome Analysis", "mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "1 cell", "GSM564428", null, "tissue:developing embryos|background:AB; wild type|developmental stage:just fertilized 1cell embryos", "1 cell", "ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.", "developing embryos", "Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.", "mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.", "Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.", "background:AB; wild type|developmental stage:just fertilized 1cell embryos", "GSM564428", "GSM564428: 1 cell", "GSM564428: 1 cell", "GSM564428: 1 cell", "1", null, "GEO Accession:GSM564428", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>", "SRP003165", null, null, null, null, 1175348550.0, 23506971.0, "GSM564428 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025026", "SRS085805", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.75876, null, 0.05232, null, 0.86762, null, 0.50392, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36685, "SRR801688", "SRX258168", "SRS406299", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish 1 wpf larvae", "GSM1112163: larva  1 week", "GSM1112163", null, "strain:AB|developmental stage:larva  1 week|tissue:larva", "larva  1 week", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish 1 wpf larvae", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:larva  1 week|tissue:larva", "GSM1112163", "GSM1112163: larva  1 week; Danio rerio; RNA Seq", "GSM1112163 1", null, "1", null, "GEO Accession:GSM1112163", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_1week_F3.csfasta.bz2 D_rerio_1week_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 18866346300.0, 377326926.0, "GSM1112163 r1", "0:50", "0:4319577052;1:5210931849;2:5202393345;3:4013865803;.:119578251", 50, null, null, null, null, null, null, null, null, "SRX258168", "SRS406299", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.60649, null, 0.05524, null, 0.86746, null, 0.51092, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [36686, "SRR801687", "SRX258167", "SRS406298", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the Protruding mouth stage", "GSM1112162: Protruding mouth  72hpf", "GSM1112162", null, "strain:AB|developmental stage:Protruding mouth  72hpf|tissue:embryo", "Protruding mouth  72hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the Protruding mouth stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:Protruding mouth  72hpf|tissue:embryo", "GSM1112162", "GSM1112162: Protruding mouth  72hpf; Danio rerio; RNA Seq", "GSM1112162 1", null, "1", null, "GEO Accession:GSM1112162", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_72hpf_F3.csfasta.bz2 D_rerio_72hpf_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 19339397750.0, 386787955.0, "GSM1112162 r1", "0:50", "0:4755453154;1:5011845177;2:5110574744;3:4002085043;.:459439632", 50, null, null, null, null, null, null, null, null, "SRX258167", "SRS406298", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.34099, null, 0.03045, null, 0.92409, null, 0.49783, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [36687, "SRR801685", "SRX258166", "SRS406297", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the Pec fin stage", "GSM1112161: Pec fin  60hpf", "GSM1112161", null, "strain:AB|developmental stage:Pec fin  60hpf|tissue:embryo", "Pec fin  60hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the Pec fin stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:Pec fin  60hpf|tissue:embryo", "GSM1112161", "GSM1112161: Pec fin  60hpf; Danio rerio; RNA Seq", "GSM1112161 1", null, "1", null, "GEO Accession:GSM1112161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_60hpf_rep1_F3_QV.qual.bz2 D_rerio_60hpf_rep1_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 14061264450.0, 281225289.0, "GSM1112161 r1", "0:50", "0:3272552510;1:3838757055;2:3984098731;3:2865843173;.:100012981", 50, null, null, null, null, null, null, null, null, "SRX258166", "SRS406297", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.64298, null, 0.04687, null, 0.8452, null, 0.50527, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36688, "SRR801686", "SRX258166", "SRS406297", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the Pec fin stage", "GSM1112161: Pec fin  60hpf", "GSM1112161", null, "strain:AB|developmental stage:Pec fin  60hpf|tissue:embryo", "Pec fin  60hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the Pec fin stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:Pec fin  60hpf|tissue:embryo", "GSM1112161", "GSM1112161: Pec fin  60hpf; Danio rerio; RNA Seq", "GSM1112161 1", null, "1", null, "GEO Accession:GSM1112161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_60hpf_rep2_F3.csfasta.bz2 D_rerio_60hpf_rep2_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 4988485300.0, 99769706.0, "GSM1112161 r2", "0:50", "0:1195740374;1:1346591727;2:1390300069;3:1024571482;.:31281648", 50, null, null, null, null, null, null, null, null, "SRX258166", "SRS406297", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.65039, null, 0.04382, null, 0.84463, null, 0.50042, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36689, "SRR801684", "SRX258165", "SRS406296", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the Long pec stage", "GSM1112160: Long pec  48hpf", "GSM1112160", null, "strain:AB|developmental stage:Long pec  48hpf|tissue:embryo", "Long pec  48hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the Long pec stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:Long pec  48hpf|tissue:embryo", "GSM1112160", "GSM1112160: Long pec  48hpf; Danio rerio; RNA Seq", "GSM1112160 1", null, "1", null, "GEO Accession:GSM1112160", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_48hpf_F3.csfasta.bz2 D_rerio_48hpf_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 18932266250.0, 378645325.0, "GSM1112160 r1", "0:50", "0:4346139923;1:5132091383;2:5261012454;3:4060753494;.:132268996", 50, null, null, null, null, null, null, null, null, "SRX258165", "SRS406296", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.59799, null, 0.03168, null, 0.87787, null, 0.49407, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36690, "SRR801683", "SRX258164", "SRS406295", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the Prim 25 stage", "GSM1112159: Prim 25  36hpf", "GSM1112159", null, "strain:AB|developmental stage:Prim 25  36hpf|tissue:embryo", "Prim 25  36hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the Prim 25 stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:Prim 25  36hpf|tissue:embryo", "GSM1112159", "GSM1112159: Prim 25  36hpf; Danio rerio; RNA Seq", "GSM1112159 1", null, "1", null, "GEO Accession:GSM1112159", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_36hpf_F3.csfasta.bz2 D_rerio_36hpf_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 17101319300.0, 342026386.0, "GSM1112159 r1", "0:50", "0:3937246171;1:4674442353;2:4750820696;3:3639194318;.:99615762", 50, null, null, null, null, null, null, null, null, "SRX258164", "SRS406295", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.64605, null, 0.05087, null, 0.86454, null, 0.49193, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36691, "SRR801682", "SRX258163", "SRS406294", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the 15 somite stage", "GSM1112158: 15 somite  16.5 17.5hpf", "GSM1112158", null, "strain:AB|developmental stage:15 somite  16.5 17.5hpf|tissue:embryo", "15 somite  16.5 17.5hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the 15 somite stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:15 somite  16.5 17.5hpf|tissue:embryo", "GSM1112158", "GSM1112158: 15 somite  16.5 17.5hpf; Danio rerio; RNA Seq", "GSM1112158 1", null, "1", null, "GEO Accession:GSM1112158", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_15somite_F3_QV.qual.bz2 D_rerio_15somite_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 19881065650.0, 397621313.0, "GSM1112158 r1", "0:50", "0:4616309398;1:5374070017;2:5493789005;3:4261458107;.:135439123", 50, null, null, null, null, null, null, null, null, "SRX258163", "SRS406294", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.65251, null, 0.04145, null, 0.8803, null, 0.49159, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36692, "SRR801681", "SRX258162", "SRS406293", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the 50% epiboly stage", "GSM1112157: 50% epiboly  5.25hpf", "GSM1112157", null, "strain:AB|developmental stage:50% epiboly  5.25hpf|tissue:embryo", "50% epiboly  5.25hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the 50% epiboly stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:50% epiboly  5.25hpf|tissue:embryo", "GSM1112157", "GSM1112157: 50% epiboly  5.25hpf; Danio rerio; RNA Seq", "GSM1112157 1", null, "1", null, "GEO Accession:GSM1112157", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_50epiboly_F3.csfasta.bz2 D_rerio_50epiboly_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 18813904400.0, 376278088.0, "GSM1112157 r1", "0:50", "0:4325556677;1:5167803890;2:5309373134;3:4011170699;.:0", 50, null, null, null, null, null, null, null, null, "SRX258162", "SRS406293", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.6164, null, 0.05047, null, 0.89767, null, 0.50223, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36693, "SRR801680", "SRX258161", "SRS406292", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the oblong sphere stage", "GSM1112156: oblong sphere  3.6 4hpf", "GSM1112156", null, "strain:AB|developmental stage:oblong sphere  3.6 4hpf|tissue:embryo", "oblong sphere  3.6 4hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the oblong sphere stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:oblong sphere  3.6 4hpf|tissue:embryo", "GSM1112156", "GSM1112156: oblong sphere  3.6 4hpf; Danio rerio; RNA Seq", "GSM1112156 1", null, "1", null, "GEO Accession:GSM1112156", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_oblong_sphere_F3.csfasta.bz2 D_rerio_oblong_sphere_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 16938508000.0, 338770160.0, "GSM1112156 r1", "0:50", "0:3947082853;1:4563069432;2:4709732005;3:3599468311;.:119155399", 50, null, null, null, null, null, null, null, null, "SRX258161", "SRS406292", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.60716, null, 0.02545, null, 0.85186, null, 0.48927, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36694, "SRR801679", "SRX258160", "SRS406291", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the 64 cell stage", "GSM1112155: 64 cell  2 hpf", "GSM1112155", null, "strain:AB|developmental stage:64 cell  2 hpf|tissue:embryo", "64 cell  2 hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the 64 cell stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:64 cell  2 hpf|tissue:embryo", "GSM1112155", "GSM1112155: 64 cell  2 hpf; Danio rerio; RNA Seq", "GSM1112155 1", null, "1", null, "GEO Accession:GSM1112155", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_64cell_F3.csfasta.bz2 D_rerio_64cell_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 11793112050.0, 235862241.0, "GSM1112155 r1", "0:50", "0:2729453191;1:3189868180;2:3325229431;3:2482063391;.:66497857", 50, null, null, null, null, null, null, null, null, "SRX258160", "SRS406291", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.56575, null, 0.01697, null, 0.8538, null, 0.48681, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37907, "SRR1104969", "SRX424037", "SRS527958", "SRP035264", "PRJNA236557", "Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]", "GSE53758", "Transcriptome Analysis", "To determine the global impact of the clbn mutation on gene expression and efficiency of U2  and U12 type splicing  we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each  genotyped homozygous wildtype and homozygous clbns841 mutants  respectively", "parent bioproject:PRJNA236230", "pubmed:24516132", null, "108hpf clbn", "GSM1303831", null, "source name:108hpf clbn larvae|genotype/variation:clbns841|development stage:108 hpf|tissue:whole larvae", "108hpf clbn", "50bp single end reads were mapped  using the X MATE recursive mapping pipeline 42  allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis  RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis  RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9", "108hpf clbn larvae", "Starting at 24 hpf  embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "Embryos for all experiments were produced by natural spawning  transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5\u00b0C incubator on a 12h light/dark cycle.", "genotype/variation:clbns841|developmental stage:108 hpf|tissue:whole larvae", "GSM1303831", "GSM1303831: 108hpf clbn; Danio rerio; RNA Seq", "GSM1303831", null, "1", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "GEO Accession:GSM1303831", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP035264", null, null, "108hpf_clbn_F3_QV.qual.bz2 108hpf_clbn_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 2698882700.0, 53977654.0, "GSM1303831 r1", "0:50", "0:653022205;1:711705790;2:753066133;3:571973990;.:9114582", 50, null, null, null, null, null, null, null, null, "SRX424037", "SRS527958", "SRA123959", "GEO", "Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research", 1, 0.56134, null, 0.05842, null, 0.84303, null, 0.49093, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2014-01-09", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [37908, "SRR1104968", "SRX424036", "SRS527957", "SRP035264", "PRJNA236557", "Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]", "GSE53758", "Transcriptome Analysis", "To determine the global impact of the clbn mutation on gene expression and efficiency of U2  and U12 type splicing  we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each  genotyped homozygous wildtype and homozygous clbns841 mutants  respectively", "parent bioproject:PRJNA236230", "pubmed:24516132", null, "108hpf wt", "GSM1303830", null, "source name:108hpf wt larvae|genotype/variation:wildtype|development stage:108 hpf|tissue:whole larvae", "108hpf wt", "50bp single end reads were mapped  using the X MATE recursive mapping pipeline 42  allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis  RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis  RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9", "108hpf wt larvae", "Starting at 24 hpf  embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "Embryos for all experiments were produced by natural spawning  transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5\u00b0C incubator on a 12h light/dark cycle.", "genotype/variation:wildtype|developmental stage:108 hpf|tissue:whole larvae", "GSM1303830", "GSM1303830: 108hpf wt; Danio rerio; RNA Seq", "GSM1303830", null, "1", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "GEO Accession:GSM1303830", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP035264", null, null, "108hpf_wt_F3_QV.qual.bz2 108hpf_wt_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 2835473700.0, 56709474.0, "GSM1303830 r1", "0:50", "0:697915785;1:748317376;2:781024795;3:605838541;.:2377203", 50, null, null, null, null, null, null, null, null, "SRX424036", "SRS527957", "SRA123959", "GEO", "Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research", 1, 0.57033, null, 0.05759, null, 0.8384, null, 0.49692, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2014-01-09", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 17, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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"submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select 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, 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