{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"generic-scrnaseq-only\", tissue_curation = \"Multi-tissue\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[60001, "SRR12083659", "SRX8610753", "SRS6900398", "SRP268708", "PRJNA641707", "Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish", "GSE153197", "Transcriptome Analysis", "Thyroid follicular cells TFCs are responsible for generation  storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al.  bioRxiv  2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly  TFC displayed transcriptional heterogeneity in the expression of pax2a  a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity  we generated a pax2a knock in line  in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in  we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep\u2122 RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome  GRCz11  using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:33140917", null, "Pax2a High TFC 3", "GSM4635496", null, "tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a High mKO2 High", "Pax2a High TFC 3", "Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file", "Thyroid Follicular Cells TFCs", null, "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", null, "age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a High mKO2 High", "GSM4635496", "GSM4635496: Pax2a High TFC 3; Danio rerio; RNA Seq", "GSM4635496", null, "1", "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", "GEO Accession:GSM4635496", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP268708", null, null, "Pax2a-highset3_S14_R1_001.fastq.gz Pax2a-highset3_S14_R2_001.fastq.gz", "fastq fastq", 16108716672.0, 80176158.0, "GSM4635496 r1", "0:100.44 1:100.48", "A:4075320644;C:4124512580;G:3756402856;T:4151374263;N:1106329", 100, 100, null, null, 4075320644, 4124512580, 3756402856, 4151374263, 1106329, "SRX8610753", "SRS6900398", "SRA1090834", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.53855, 0.55508, 0.21647, 0.22708, 0.82775, 0.82838, 0.43125, 0.42144, 101, 100, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Belgium", "2020-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [60002, "SRR12083658", "SRX8610752", "SRS6900397", "SRP268708", "PRJNA641707", "Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish", "GSE153197", "Transcriptome Analysis", "Thyroid follicular cells TFCs are responsible for generation  storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al.  bioRxiv  2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly  TFC displayed transcriptional heterogeneity in the expression of pax2a  a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity  we generated a pax2a knock in line  in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in  we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep\u2122 RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome  GRCz11  using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:33140917", null, "Pax2a Low TFC 3", "GSM4635495", null, "tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low", "Pax2a Low TFC 3", "Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file", "Thyroid Follicular Cells TFCs", null, "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", null, "age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low", "GSM4635495", "GSM4635495: Pax2a Low TFC 3; Danio rerio; RNA Seq", "GSM4635495", null, "1", "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", "GEO Accession:GSM4635495", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP268708", null, null, "Pax2a-lowset3_S13_R2_001.fastq.gz Pax2a-lowset3_S13_R1_001.fastq.gz", "fastq fastq", 15927464315.0, 79263861.0, "GSM4635495 r1", "0:100.42 1:100.53", "A:3806928663;C:4340989624;G:3919724503;T:3858828310;N:993215", 100, 100, null, null, 3806928663, 4340989624, 3919724503, 3858828310, 993215, "SRX8610752", "SRS6900397", "SRA1090834", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.18449, 0.18221, 0.07867, 0.07638, 0.91488, 0.91419, 0.61183, 0.60137, 100, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Belgium", "2020-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [60003, "SRR12083657", "SRX8610751", "SRS6900396", "SRP268708", "PRJNA641707", "Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish", "GSE153197", "Transcriptome Analysis", "Thyroid follicular cells TFCs are responsible for generation  storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al.  bioRxiv  2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly  TFC displayed transcriptional heterogeneity in the expression of pax2a  a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity  we generated a pax2a knock in line  in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in  we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep\u2122 RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome  GRCz11  using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:33140917", null, "Pax2a High TFC 2", "GSM4635494", null, "tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a High mKO2 High", "Pax2a High TFC 2", "Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file", "Thyroid Follicular Cells TFCs", null, "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", null, "age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a High mKO2 High", "GSM4635494", "GSM4635494: Pax2a High TFC 2; Danio rerio; RNA Seq", "GSM4635494", null, "1", "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", "GEO Accession:GSM4635494", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP268708", null, null, "Pax2a-highset2_S12_R1_001.fastq.gz Pax2a-highset2_S12_R2_001.fastq.gz", "fastq fastq", 15523399241.0, 77253456.0, "GSM4635494 r1", "0:100.43 1:100.51", "A:3874954294;C:4043105713;G:3665233417;T:3939083016;N:1022801", 100, 100, null, null, 3874954294, 4043105713, 3665233417, 3939083016, 1022801, "SRX8610751", "SRS6900396", "SRA1090834", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.33224, 0.33308, 0.1301, 0.13243, 0.87411, 0.8732, 0.45849, 0.46552, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Belgium", "2020-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [60004, "SRR12083656", "SRX8610750", "SRS6900395", "SRP268708", "PRJNA641707", "Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish", "GSE153197", "Transcriptome Analysis", "Thyroid follicular cells TFCs are responsible for generation  storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al.  bioRxiv  2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly  TFC displayed transcriptional heterogeneity in the expression of pax2a  a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity  we generated a pax2a knock in line  in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in  we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep\u2122 RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome  GRCz11  using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:33140917", null, "Pax2a Low TFC 2", "GSM4635493", null, "tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low", "Pax2a Low TFC 2", "Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file", "Thyroid Follicular Cells TFCs", null, "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", null, "age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low", "GSM4635493", "GSM4635493: Pax2a Low TFC 2; Danio rerio; RNA Seq", "GSM4635493", null, "1", "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", "GEO Accession:GSM4635493", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP268708", null, null, "Pax2a-lowset2_S11_R2_001.fastq.gz Pax2a-lowset2_S11_R1_001.fastq", "fastq fastq", 14562196360.0, 85940573.0, "GSM4635493 r1", "0:100.38 1:100.53", "A:3643644077;C:3784618122;G:3352785620;T:3780129729;N:1018812", 100, 100, null, null, 3643644077, 3784618122, 3352785620, 3780129729, 1018812, "SRX8610750", "SRS6900395", "SRA1090834", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.16299, 0.15776, 0.06375, 0.06201, 0.93162, 0.93117, 0.63175, 0.62162, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Belgium", "2020-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [60005, "SRR12083655", "SRX8610749", "SRS6900394", "SRP268708", "PRJNA641707", "Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish", "GSE153197", "Transcriptome Analysis", "Thyroid follicular cells TFCs are responsible for generation  storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al.  bioRxiv  2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly  TFC displayed transcriptional heterogeneity in the expression of pax2a  a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity  we generated a pax2a knock in line  in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in  we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep\u2122 RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome  GRCz11  using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:33140917", null, "Pax2a High TFC 1", "GSM4635492", null, "tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a High mKO2 High", "Pax2a High TFC 1", "Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file", "Thyroid Follicular Cells TFCs", null, "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", null, "age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a High mKO2 High", "GSM4635492", "GSM4635492: Pax2a High TFC 1; Danio rerio; RNA Seq", "GSM4635492", null, "1", "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", "GEO Accession:GSM4635492", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP268708", null, null, "Pax2a-highset1_S10_R1_001.fastq.gz Pax2a-highset1_S10_R2_001.fastq.gz", "fastq fastq", 16402884907.0, 81622449.0, "GSM4635492 r1", "0:100.45 1:100.51", "A:4148895557;C:4226508291;G:3782541016;T:4243916995;N:1023048", 100, 100, null, null, 4148895557, 4226508291, 3782541016, 4243916995, 1023048, "SRX8610749", "SRS6900394", "SRA1090834", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.25304, 0.25554, 0.09753, 0.10045, 0.89986, 0.89936, 0.4275, 0.41328, 101, 99, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Belgium", "2020-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [60006, "SRR12083654", "SRX8610748", "SRS6900393", "SRP268708", "PRJNA641707", "Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish", "GSE153197", "Transcriptome Analysis", "Thyroid follicular cells TFCs are responsible for generation  storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al.  bioRxiv  2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly  TFC displayed transcriptional heterogeneity in the expression of pax2a  a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity  we generated a pax2a knock in line  in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in  we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep\u2122 RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome  GRCz11  using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.", null, "pubmed:33140917", null, "Pax2a Low TFC 1", "GSM4635491", null, "tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low", "Pax2a Low TFC 1", "Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file", "Thyroid Follicular Cells TFCs", null, "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", null, "age:5 mpf|genotype/variation:Tgtg:nls EGFP  pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low", "GSM4635491", "GSM4635491: Pax2a Low TFC 1; Danio rerio; RNA Seq", "GSM4635491", null, "1", "Enzymatic Dissociation Ribozyme depletion  adapter ligation  followed by llumina NextSeq500", "GEO Accession:GSM4635491", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP268708", null, null, "Pax2a-lowset1_S9_R1_001.fastq.gz Pax2a-lowset1_S9_R2_001.fastq.gz", "fastq fastq", 17841813800.0, 88772569.0, "GSM4635491 r1", "0:100.47 1:100.51", "A:4653492569;C:4489464840;G:4023148591;T:4674617491;N:1090309", 100, 100, null, null, 4653492569, 4489464840, 4023148591, 4674617491, 1090309, "SRX8610748", "SRS6900393", "SRA1090834", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.08055, 0.07962, 0.02812, 0.02691, 0.96126, 0.96126, 0.67769, 0.72985, 100, 101, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Belgium", "2020-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [68079, "SRR17604930", "SRX13773746", "SRS11653747", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt Ctrl rep3", "GSM5814820", null, "tissue:epithelial|age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "Krt Ctrl rep3", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814820", "GSM5814820: Krt Ctrl rep3; Danio rerio; RNA Seq", "GSM5814820 r1", "GSM5814820", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "D9_AAGAGG_L007_R1_001.fastq.gz", "fastq", 1119889717.0, 11088017.0, "GSM5814820 r1", "0:101 1:0", "A:268013821;C:268948711;G:354482020;T:228355242;N:89923", 101, 0, null, null, 268013821, 268948711, 354482020, 228355242, 89923, "SRX13773746", "SRS11653747", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.83634, null, 0.25142, null, 0.92107, null, 0.73967, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68080, "SRR17604931", "SRX13773746", "SRS11653747", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt Ctrl rep3", "GSM5814820", null, "tissue:epithelial|age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "Krt Ctrl rep3", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814820", "GSM5814820: Krt Ctrl rep3; Danio rerio; RNA Seq", "GSM5814820 r1", "GSM5814820", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "D9_AAGAGG_L008_R1_001.fastq.gz", "fastq", 1107311076.0, 10963476.0, "GSM5814820 r2", "0:101 1:0", "A:265076502;C:265784761;G:350224779;T:226169505;N:55529", 101, 0, null, null, 265076502, 265784761, 350224779, 226169505, 55529, "SRX13773746", "SRS11653747", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.83676, null, 0.25471, null, 0.92172, null, 0.75036, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68085, "SRR17604936", "SRX13773743", "SRS11653744", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt V12 rep3", "GSM5814817", null, "tissue:epithelial|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "Krt V12 rep3", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814817", "GSM5814817: Krt V12 rep3; Danio rerio; RNA Seq", "GSM5814817 r1", "GSM5814817", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "d12_GAGTCA_L007_R1_001.fastq.gz", "fastq", 1293081083.0, 12802783.0, "GSM5814817 r1", "0:101 1:0", "A:294765651;C:315869756;G:422506461;T:259837016;N:102199", 101, 0, null, null, 294765651, 315869756, 422506461, 259837016, 102199, "SRX13773743", "SRS11653744", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.86334, null, 0.24183, null, 0.8915, null, 0.71576, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68086, "SRR17604937", "SRX13773743", "SRS11653744", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt V12 rep3", "GSM5814817", null, "tissue:epithelial|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "Krt V12 rep3", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814817", "GSM5814817: Krt V12 rep3; Danio rerio; RNA Seq", "GSM5814817 r1", "GSM5814817", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "d12_GAGTCA_L008_R1_001.fastq.gz", "fastq", 1275303871.0, 12626771.0, "GSM5814817 r2", "0:101 1:0", "A:290705038;C:311345036;G:416458015;T:256730885;N:64897", 101, 0, null, null, 290705038, 311345036, 416458015, 256730885, 64897, "SRX13773743", "SRS11653744", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.86353, null, 0.24248, null, 0.89025, null, 0.73082, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68091, "SRR17604942", "SRX13773740", "SRS11653741", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt Ctrl rep2", "GSM5814814", null, "tissue:epithelial|age:3dpf|batch:2|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "Krt Ctrl rep2", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:2|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814814", "GSM5814814: Krt Ctrl rep2; Danio rerio; RNA Seq", "GSM5814814 r1", "GSM5814814", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "C9_AAGCCT_L007_R1_001.fastq.gz", "fastq", 2009406817.0, 19895117.0, "GSM5814814 r1", "0:101 1:0", "A:438640008;C:494033974;G:682135581;T:394568602;N:28652", 101, 0, null, null, 438640008, 494033974, 682135581, 394568602, 28652, "SRX13773740", "SRS11653741", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.88893, null, 0.24477, null, 0.94992, null, 0.77184, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68094, "SRR17604945", "SRX13773737", "SRS11653738", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt V12 rep2", "GSM5814811", null, "tissue:epithelial|age:3dpf|batch:2|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "Krt V12 rep2", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:2|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814811", "GSM5814811: Krt V12 rep2; Danio rerio; RNA Seq", "GSM5814811 r1", "GSM5814811", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "C12_GGAGAA_L007_R1_001.fastq.gz", "fastq", 2120385617.0, 20993917.0, "GSM5814811 r1", "0:101 1:0", "A:468255703;C:520073226;G:720772615;T:411253641;N:30432", 101, 0, null, null, 468255703, 520073226, 720772615, 411253641, 30432, "SRX13773737", "SRS11653738", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.89927, null, 0.21831, null, 0.95373, null, 0.71636, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68097, "SRR17604948", "SRX13773734", "SRS11653735", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt Ctrl rep1", "GSM5814808", null, "tissue:epithelial|age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "Krt Ctrl rep1", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814808", "GSM5814808: Krt Ctrl rep1; Danio rerio; RNA Seq", "GSM5814808 r1", "GSM5814808", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. 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Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt Ctrl rep1", "GSM5814808", null, "tissue:epithelial|age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "Krt Ctrl rep1", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814808", "GSM5814808: Krt Ctrl rep1; Danio rerio; RNA Seq", "GSM5814808 r1", "GSM5814808", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. 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Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt V12 rep1", "GSM5814805", null, "tissue:epithelial|age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "Krt V12 rep1", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814805", "GSM5814805: Krt V12 rep1; Danio rerio; RNA Seq", "GSM5814805 r1", "GSM5814805", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "B12_GTCGTA_L003_R1_001.fastq.gz", "fastq", 1279886443.0, 12672143.0, "GSM5814805 r1", "0:101 1:0", "A:287939360;C:312300654;G:420407313;T:259182902;N:56214", 101, 0, null, null, 287939360, 312300654, 420407313, 259182902, 56214, "SRX13773731", "SRS11653732", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.89701, null, 0.22936, null, 0.9275, null, 0.76668, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [68104, "SRR17604955", "SRX13773731", "SRS11653732", "SRP354901", "PRJNA796794", "Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation", "GSE193591", "Transcriptome Analysis", "We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types", null, "pubmed:35250998", null, "Krt V12 rep1", "GSM5814805", null, "tissue:epithelial|age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "Krt V12 rep1", "Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "epithelial", "Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V\u00a0constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into\u00a0TgLyzC:EGFP L10a\u00a0or\u00a0Tgmpeg1:EGFP L10a\u00a0larvae\u00a0for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively.\u00a0", "Larvae were stored at  80\u00b0C in minimal residual media.\u00a0QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200\u00a0pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer\u2019s protocols.", null, "age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312", "GSM5814805", "GSM5814805: Krt V12 rep1; Danio rerio; RNA Seq", "GSM5814805 r1", "GSM5814805", "1", "Larvae were stored at  80\u00b0C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration\u2009<\u2009200 pg/\u00b5l were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354901", null, null, "B12_GTCGTA_L004_R1_001.fastq.gz", "fastq", 1292551237.0, 12797537.0, "GSM5814805 r2", "0:101 1:0", "A:290587833;C:315368331;G:424558613;T:261915584;N:120876", 101, 0, null, null, 290587833, 315368331, 424558613, 261915584, 120876, "SRX13773731", "SRS11653732", "SRA1356563", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 1, 0.89789, null, 0.23117, null, 0.92843, null, 0.77165, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2022-01-13", "Larval", "Larval", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 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