{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and tissue_curation = \"Spleen\"", "rows": [[38293, "SRR1647684", "SRX756919", "SRS742121", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "24S", "GSM1541908", null, "source name:spleen|tissue:spleen|disease state:24h post SVCV infection", "24S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:24h post SVCV infection", "GSM1541908", "GSM1541908: 24S; Danio rerio; RNA Seq", "GSM1541908", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541908", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "24S_ATGTCA_L003_R1.fastq", "fastq", 1207014756.0, 23666956.0, "GSM1541908 r1", "0:51", "A:316359100;C:290453604;G:283305513;T:316815698;N:80841", 51, null, null, null, 316359100, 290453604, 283305513, 316815698, 80841, "SRX756919", "SRS742121", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.91158, null, 0.09021, null, 0.70867, null, 0.46907, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [38294, "SRR1647683", "SRX756918", "SRS742119", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "6S", "GSM1541907", null, "source name:spleen|tissue:spleen|disease state:6h post SVCV infection", "6S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:6h post SVCV infection", "GSM1541907", "GSM1541907: 6S; Danio rerio; RNA Seq", "GSM1541907", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541907", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "6S_AGTTCC_L003_R1.fastq", "fastq", 1251006540.0, 24529540.0, "GSM1541907 r1", "0:51", "A:323805792;C:303846999;G:297418642;T:325862442;N:72665", 51, null, null, null, 323805792, 303846999, 297418642, 325862442, 72665, "SRX756918", "SRS742119", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92105, null, 0.09005, null, 0.71273, null, 0.46937, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [38295, "SRR1647682", "SRX756917", "SRS742118", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "0S", "GSM1541906", null, "source name:spleen|tissue:spleen|disease state:un infected", "0S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:un infected", "GSM1541906", "GSM1541906: 0S; Danio rerio; RNA Seq", "GSM1541906", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541906", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "0S_AGTCAA_L003_R1.fastq", "fastq", 1155087372.0, 22648772.0, "GSM1541906 r1", "0:51", "A:301183546;C:279328135;G:272663981;T:301834798;N:76912", 51, null, null, null, 301183546, 279328135, 272663981, 301834798, 76912, "SRX756917", "SRS742118", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.91841, null, 0.09679, null, 0.70546, null, 0.47624, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [52200, "SRR8991406", "SRX5770474", "SRS4704583", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.", null, "pubmed:34660600", null, "Spleen3", "GSM3740959", null, "source name:spleen|strain:Tubingen|genotype:wild type|tissue:spleen", "Spleen3", "The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.", "spleen", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype:wild type|tissue:spleen", "GSM3740959", "GSM3740959: Spleen3; Danio rerio; RNA Seq", "GSM3740959", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3740959", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10", "Spleen3.bam", "bam", 29617062386.0, 98069743.0, "GSM3740959 r1", "0:151 1:151", "A:7464139749;C:4972084318;G:5132144813;T:11970808438;N:77885068", 151, 151, null, null, 7464139749, 4972084318, 5132144813, 11970808438, 77885068, "SRX5770474", "SRS4704583", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.7261, 0.0, 0.03774, 1.0, 0.86275, null, 0.5339, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-04-30", "Undetermined", "Multi-stage", "Spleen", "Hematopoietic System"], [63895, "SRR14213371", "SRX10579916", "SRS8684384", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Spleen3", "GSM5237140", null, "source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB", "Spleen3", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish spleen", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:spleen|strain:TLAB", "GSM5237140", "GSM5237140: Spleen3; Danio rerio; RNA Seq", "GSM5237140", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Spleen3.fastq", "fastq", 2469245600.0, 24692456.0, "GSM5237140 r1", "0:100", "A:595265067;C:649103304;G:625399353;T:599383209;N:94667", 100, null, null, null, 595265067, 649103304, 625399353, 599383209, 94667, "SRX10579916", "SRS8684384", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9388, null, 0.16508, null, 0.75205, null, 0.59719, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [63896, "SRR14213370", "SRX10579915", "SRS8684383", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Spleen2", "GSM5237139", null, "source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB", "Spleen2", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish spleen", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:spleen|strain:TLAB", "GSM5237139", "GSM5237139: Spleen2; Danio rerio; RNA Seq", "GSM5237139", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Spleen2.fastq", "fastq", 1372663100.0, 13726631.0, "GSM5237139 r1", "0:100", "A:303080845;C:392345861;G:369765807;T:307418421;N:52166", 100, null, null, null, 303080845, 392345861, 369765807, 307418421, 52166, "SRX10579915", "SRS8684383", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96541, null, 0.18478, null, 0.78565, null, 0.60522, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [63897, "SRR14213369", "SRX10579914", "SRS8684382", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Spleen1", "GSM5237138", null, "source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB", "Spleen1", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish spleen", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:spleen|strain:TLAB", "GSM5237138", "GSM5237138: Spleen1; Danio rerio; RNA Seq", "GSM5237138", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Spleen1.fastq", "fastq", 2268815600.0, 22688156.0, "GSM5237138 r1", "0:100", "A:570901318;C:562128594;G:552921437;T:582778510;N:85741", 100, null, null, null, 570901318, 562128594, 552921437, 582778510, 85741, "SRX10579914", "SRS8684382", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93633, null, 0.14981, null, 0.72825, null, 0.52073, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71972, "SRR22163682", "SRX18142568", "SRS15644032", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "C3", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:control|replicate:replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "C3", "C3", "control group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "C3.R1.fastq.gz C3.R2.fastq.gz", "fastq fastq", 6777299176.0, 22441388.0, "C3.R1.fastq.gz", "0:151 1:151", "A:1869146927;C:1513142912;G:1565477798;T:1829395893;N:135646", 151, 151, null, null, 1869146927, 1513142912, 1565477798, 1829395893, 135646, "SRX18142568", "SRS15644032", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.91581, 0.91452, 0.09416, 0.09344, 0.71167, 0.71338, 0.50247, 0.50311, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71973, "SRR22163683", "SRX18142567", "SRS15644031", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "C2", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:control|replicate:replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "C2", "C2", "control group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "C2.R1.fastq.gz C2.R2.fastq.gz", "fastq fastq", 6956425644.0, 23034522.0, "C2.R1.fastq.gz", "0:151 1:151", "A:1847551873;C:1616308106;G:1662475314;T:1829952767;N:137584", 151, 151, null, null, 1847551873, 1616308106, 1662475314, 1829952767, 137584, "SRX18142567", "SRS15644031", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93033, 0.9312, 0.056, 0.05619, 0.71261, 0.71376, 0.4668, 0.47014, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71974, "SRR22163684", "SRX18142566", "SRS15644030", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "C1", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:control|replicate:replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "C1", "C1", "control group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "C1.R1.fastq.gz C1.R2.fastq.gz", "fastq fastq", 6218689172.0, 20591686.0, "C1.R1.fastq.gz", "0:151 1:151", "A:1651743119;C:1444992966;G:1490934383;T:1630891482;N:127222", 151, 151, null, null, 1651743119, 1444992966, 1490934383, 1630891482, 127222, "SRX18142566", "SRS15644030", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93571, 0.93627, 0.03427, 0.0346, 0.73336, 0.73401, 0.47064, 0.47601, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71975, "SRR22163685", "SRX18142565", "SRS15644029", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "B3", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:challenge|replicate:replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "B3", "B3", "challenge group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "B3.R1.fastq.gz B3.R2.fastq.gz", "fastq fastq", 7958268062.0, 26351881.0, "B3.R1.fastq.gz", "0:151 1:151", "A:2067039750;C:1894612680;G:1943559820;T:2052891379;N:164433", 151, 151, null, null, 2067039750, 1894612680, 1943559820, 2052891379, 164433, "SRX18142565", "SRS15644029", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93754, 0.93809, 0.03309, 0.03347, 0.71762, 0.71731, 0.49012, 0.4888, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71976, "SRR22163686", "SRX18142564", "SRS15644028", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "B2", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:challenge|replicate:replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "B2", "B2", "challenge group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "B2.R1.fastq.gz B2.R2.fastq.gz", "fastq fastq", 7071097158.0, 23414229.0, "B2.R1.fastq.gz", "0:151 1:151", "A:1862299896;C:1658740196;G:1713471478;T:1836444697;N:140891", 151, 151, null, null, 1862299896, 1658740196, 1713471478, 1836444697, 140891, "SRX18142564", "SRS15644028", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.94335, 0.94369, 0.04139, 0.04172, 0.80405, 0.80415, 0.39649, 0.39674, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71977, "SRR22163687", "SRX18142563", "SRS15644027", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "B1", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:challenge|replicate:replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "B1", "B1", "challenge group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "B1.R1.fastq.gz B1.R2.fastq.gz", "fastq fastq", 7597788178.0, 25158239.0, "B1.R1.fastq.gz", "0:151 1:151", "A:1986638730;C:1797302173;G:1839273564;T:1974418679;N:155032", 151, 151, null, null, 1986638730, 1797302173, 1839273564, 1974418679, 155032, "SRX18142563", "SRS15644027", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93891, 0.93921, 0.04922, 0.04888, 0.74552, 0.74501, 0.48725, 0.49058, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71978, "SRR22163688", "SRX18142562", "SRS15644026", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "A3", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:treatment|replicate:replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "A3", "A3", "treatment group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "A3.R1.fastq.gz A3.R2.fastq.gz", "fastq fastq", 8674550152.0, 28723676.0, "A3.R1.fastq.gz", "0:151 1:151", "A:2234032232;C:2083164440;G:2128058461;T:2229111717;N:183302", 151, 151, null, null, 2234032232, 2083164440, 2128058461, 2229111717, 183302, "SRX18142562", "SRS15644026", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93839, 0.93828, 0.01889, 0.01887, 0.73639, 0.73724, 0.48841, 0.47397, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71979, "SRR22163689", "SRX18142561", "SRS15644025", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "A2", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:treatment|replicate:replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "A2", "A2", "treatment group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "A2.R1.fastq.gz A2.R2.fastq.gz", "fastq fastq", 7383660816.0, 24449208.0, "A2.R1.fastq.gz", "0:151 1:151", "A:1917884453;C:1759507724;G:1796259178;T:1909857526;N:151935", 151, 151, null, null, 1917884453, 1759507724, 1796259178, 1909857526, 151935, "SRX18142561", "SRS15644025", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93853, 0.93854, 0.02662, 0.02663, 0.71435, 0.7149, 0.49509, 0.49212, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [71980, "SRR22163690", "SRX18142560", "SRS15644024", "SRP405990", "PRJNA897077", "Transcriptome of zebrafish Danio rerio", "PRJNA897077", "Other", "Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now  the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics  we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.", null, null, null, null, "A1", null, "strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:treatment|replicate:replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "A1", "A1", "treatment group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP405990", null, null, "A1.R1.fastq.gz A1.R2.fastq.gz", "fastq fastq", 7734454352.0, 25610776.0, "A1.R1.fastq.gz", "0:151 1:151", "A:2031967267;C:1817027018;G:1866115793;T:2019187811;N:156463", 151, 151, null, null, 2031967267, 1817027018, 1866115793, 2019187811, 156463, "SRX18142560", "SRS15644024", "SRA1532870", "Kunming University of Science and Technology|Faculty of Life Science and Technology", "Kunming University of Science and Technology", 2, 0.93755, 0.93728, 0.03692, 0.03688, 0.71664, 0.71693, 0.48577, 0.48719, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-11-02", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 16, "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", "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", 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