{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Adult\" and technology = \"marsseq\"", "rows": [[68656, "SRR18097957", "SRX14248907", "SRS12068875", "SRP360907", "PRJNA809307", "Generation of specialized blood vessels via lymphatic transdifferentiation", "GSE197161", "Transcriptome Analysis", "The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the  vascular system  endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify  to cater the different physiological demands of each organ . While LVs are known to originate from  multiple origins   lymphatic ECs LECs themselves are not known to generate other cell   types . Here  we  u s e recurrent imaging and lineage   tracing of ECs in zebrafish anal fins AF from early development  through maturity   to uncover an unexpected mechanism of specialized blood vessel formation  through transdifferentiation of LECs . Moreover  we demonstrate distinct functional implications for  deriving AF vessels from either LECs or blood ECs  uncovering a link between cell ontogeny and  functionality. We further use scRNA   seq to characterize the different cellular populations and transition  states involved in the transdifferentiation process . Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate3", "GSM5910460", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate3", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2  and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt  AB007.txt  AB008.txt: expression dataset  txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file  sheet1  pool barcode of plate1  sheet2  cell barcodes and coordinates  required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file  sheet1  pool barcode of plate2  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file  sheet1  pool barcode of plate3  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "tissue:Anal fin|cell type:endothelial cells|Stage:II III", "GSM5910460", "GSM5910460: Immature fin ECs plate3; Danio rerio; RNA Seq", "GSM5910460 r1", "GSM5910460", "1", "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP360907", null, null, "BC3_S0_R1_001.fastq.gz BC3_S0_R2_001.fastq.gz", "fastq fastq", 5000226570.0, 55558073.0, "GSM5910460 r1", "0:75 1:15", "A:1398279779;C:1105834990;G:1278168650;T:1217071842;N:871309", 75, 15, null, null, 1398279779, 1105834990, 1278168650, 1217071842, 871309, "SRX14248907", "SRS12068875", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.75587, 0.0, 0.22384, 0.0, 0.87665, 1.0, 0.59533, null, 75, 15, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-02-22", "Undetermined", "Adult", "Fin", "Surface Structure"], [68657, "SRR18097958", "SRX14248906", "SRS12068874", "SRP360907", "PRJNA809307", "Generation of specialized blood vessels via lymphatic transdifferentiation", "GSE197161", "Transcriptome Analysis", "The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the  vascular system  endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify  to cater the different physiological demands of each organ . While LVs are known to originate from  multiple origins   lymphatic ECs LECs themselves are not known to generate other cell   types . Here  we  u s e recurrent imaging and lineage   tracing of ECs in zebrafish anal fins AF from early development  through maturity   to uncover an unexpected mechanism of specialized blood vessel formation  through transdifferentiation of LECs . Moreover  we demonstrate distinct functional implications for  deriving AF vessels from either LECs or blood ECs  uncovering a link between cell ontogeny and  functionality. We further use scRNA   seq to characterize the different cellular populations and transition  states involved in the transdifferentiation process . Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate2", "GSM5910459", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate2", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2  and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt  AB007.txt  AB008.txt: expression dataset  txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file  sheet1  pool barcode of plate1  sheet2  cell barcodes and coordinates  required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file  sheet1  pool barcode of plate2  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file  sheet1  pool barcode of plate3  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "tissue:Anal fin|cell type:endothelial cells|Stage:II III", "GSM5910459", "GSM5910459: Immature fin ECs plate2; Danio rerio; RNA Seq", "GSM5910459 r1", "GSM5910459", "1", "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP360907", null, null, "BC2_S0_R1_001.fastq.gz BC2_S0_R2_001.fastq.gz", "fastq fastq", 4158365400.0, 46204060.0, "GSM5910459 r1", "0:75 1:15", "A:1056133752;C:954371027;G:1117373354;T:1029764959;N:722308", 75, 15, null, null, 1056133752, 954371027, 1117373354, 1029764959, 722308, "SRX14248906", "SRS12068874", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.76282, 0.0, 0.2382, 0.0, 0.87158, 1.0, 0.53888, null, 75, 15, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-02-22", "Undetermined", "Adult", "Fin", "Surface Structure"], [68658, "SRR18097959", "SRX14248905", "SRS12068873", "SRP360907", "PRJNA809307", "Generation of specialized blood vessels via lymphatic transdifferentiation", "GSE197161", "Transcriptome Analysis", "The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the  vascular system  endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify  to cater the different physiological demands of each organ . While LVs are known to originate from  multiple origins   lymphatic ECs LECs themselves are not known to generate other cell   types . Here  we  u s e recurrent imaging and lineage   tracing of ECs in zebrafish anal fins AF from early development  through maturity   to uncover an unexpected mechanism of specialized blood vessel formation  through transdifferentiation of LECs . Moreover  we demonstrate distinct functional implications for  deriving AF vessels from either LECs or blood ECs  uncovering a link between cell ontogeny and  functionality. We further use scRNA   seq to characterize the different cellular populations and transition  states involved in the transdifferentiation process . Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate1", "GSM5910458", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate1", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2  and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt  AB007.txt  AB008.txt: expression dataset  txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file  sheet1  pool barcode of plate1  sheet2  cell barcodes and coordinates  required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file  sheet1  pool barcode of plate2  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file  sheet1  pool barcode of plate3  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "tissue:Anal fin|cell type:endothelial cells|Stage:II III", "GSM5910458", "GSM5910458: Immature fin ECs plate1; Danio rerio; RNA Seq", "GSM5910458 r1", "GSM5910458", "1", "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP360907", null, null, "BC1_S0_R1_001.fastq.gz BC1_S0_R2_001.fastq.gz", "fastq fastq", 4284501750.0, 47605575.0, "GSM5910458 r1", "0:75 1:15", "A:1172578653;C:976724863;G:1071723716;T:1062724053;N:750465", 75, 15, null, null, 1172578653, 976724863, 1071723716, 1062724053, 750465, "SRX14248905", "SRS12068873", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.73652, 0.0, 0.20176, 0.0, 0.86622, 1.0, 0.66697, null, 75, 15, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-02-22", "Undetermined", "Adult", "Fin", "Surface Structure"], [69988, "SRR19217299", "SRX15281308", "SRS13012753", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9278", "GSM6153483", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing", "AB9278", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month", "GSM6153483", "GSM6153483: AB9278; Danio rerio; RNA Seq", "GSM6153483 r1", "GSM6153483", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz", "fastq fastq", 1259447780.0, 11770540.0, "GSM6153483 r1", "0:92 1:15", "A:305608913;C:313550706;G:363197186;T:277079546;N:11429", 92, 15, null, null, 305608913, 313550706, 363197186, 277079546, 11429, "SRX15281308", "SRS13012753", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.94767, 0.0, 0.32091, 0.0, 0.89796, 1.0, 0.7545, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69989, "SRR19217300", "SRX15281307", "SRS13012752", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9277", "GSM6153482", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing", "AB9277", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month", "GSM6153482", "GSM6153482: AB9277; Danio rerio; RNA Seq", "GSM6153482 r1", "GSM6153482", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz", "fastq fastq", 1130776107.0, 10568001.0, "GSM6153482 r1", "0:92 1:15", "A:288600700;C:269726443;G:310844405;T:261594352;N:10207", 92, 15, null, null, 288600700, 269726443, 310844405, 261594352, 10207, "SRX15281307", "SRS13012752", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.94379, 0.0, 0.28638, 0.0, 0.86415, 1.0, 0.63321, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69990, "SRR19217301", "SRX15281306", "SRS13012751", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9280", "GSM6153481", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing", "AB9280", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month", "GSM6153481", "GSM6153481: AB9280; Danio rerio; RNA Seq", "GSM6153481 r1", "GSM6153481", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz", "fastq fastq", 1172966528.0, 10962304.0, "GSM6153481 r1", "0:92 1:15", "A:311089180;C:274626206;G:310304031;T:276936052;N:11059", 92, 15, null, null, 311089180, 274626206, 310304031, 276936052, 11059, "SRX15281306", "SRS13012751", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.92936, 0.0, 0.23628, 0.0, 0.86147, 1.0, 0.74656, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69991, "SRR19217302", "SRX15281305", "SRS13012750", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9279", "GSM6153480", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing", "AB9279", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month", "GSM6153480", "GSM6153480: AB9279; Danio rerio; RNA Seq", "GSM6153480 r1", "GSM6153480", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz", "fastq fastq", 1383147163.0, 12926609.0, "GSM6153480 r1", "0:92 1:15", "A:364575971;C:320901229;G:367626618;T:330030659;N:12686", 92, 15, null, null, 364575971, 320901229, 367626618, 330030659, 12686, "SRX15281305", "SRS13012750", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.92462, 0.0, 0.26743, 0.0, 0.8493, 1.0, 0.74133, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"]], "truncated": false, "filtered_table_rows_count": 7, "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", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", 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