{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Larval\" and tissue_curation = \"Gut\"", "rows": [[35, "DRR408239", "DRX393845", "DRS407003", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB larval gut replicate 3", "zebrafish larval gut replicate 3", "SAMD00529459", null, "sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529459", "DRX393845", "AR012 gut 5  5 dpf 6 dpf larvae", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529459", null, null, null, 3463982046.0, 27491921.0, "DRR408239", "0:126 1:0", "A:842552557;C:849757648;G:837664725;T:933942026;N:65090", 126, 0, null, null, 842552557, 849757648, 837664725, 933942026, 65090, "DRX393845", "DRS407003", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Larval", "Larval", "Gut", "Digestive System"], [36, "DRR408238", "DRX393844", "DRS407002", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB larval gut replicate 2", "zebrafish larval gut replicate 2", "SAMD00529458", null, "sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529458", "DRX393844", "AR005 gut 3  5 dpf 6 dpf larvae", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529458", null, null, null, 3782320416.0, 30018416.0, "DRR408238", "0:126 1:0", "A:930337206;C:920645770;G:906559955;T:1024704277;N:73208", 126, 0, null, null, 930337206, 920645770, 906559955, 1024704277, 73208, "DRX393844", "DRS407002", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Larval", "Larval", "Gut", "Digestive System"], [37, "DRR408237", "DRX393843", "DRS407001", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB larval gut replicate 1", "zebrafish larval gut replicate 1", "SAMD00529457", null, "sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529457", "DRX393843", "AR002 gut 1  5 dpf 6 dpf larvae", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529457", null, null, null, 3606885828.0, 28626078.0, "DRR408237", "0:126 1:0", "A:879148446;C:885673723;G:870330963;T:971663212;N:69484", 126, 0, null, null, 879148446, 885673723, 870330963, 971663212, 69484, "DRX393843", "DRS407001", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Larval", "Larval", "Gut", "Digestive System"], [172, "DRR075398", "DRX069312", "DRS075493", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The gut of control fish 7dpf", "Control gut", "SAMD00065412", null, "sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065412", "DRX069312", "Control gut", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065412", null, null, null, 1008093492.0, 28002597.0, "DRR075398", "0:36", "A:230431417;C:251640901;G:244174255;T:281811580;N:35339", 36, null, null, null, 230431417, 251640901, 244174255, 281811580, 35339, "DRX069312", "DRS075493", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.9173, null, 0.07181, null, 0.72017, null, 0.45193, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Gut", "Digestive System"], [30694, "SRR28272066", "SRX23882001", "SRS20705714", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122775  HuNoV infected  replicate 2 scRNAseq", "GSM8136771", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122775  HuNoV infected  replicate 2 scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136771", "GSM8136771: GC122775  HuNoV infected  replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM8136771 r1", "GSM8136771", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz", "fastq fastq", 6487168261.0, 54514019.0, "GSM8136771 r1", "0:28 1:91", "A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286", 28, 91, null, null, 1754199332, 1533792234, 1687916105, 1511168304, 92286, "SRX23882001", "SRS20705714", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30695, "SRR28272067", "SRX23882001", "SRS20705714", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122775  HuNoV infected  replicate 2 scRNAseq", "GSM8136771", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122775  HuNoV infected  replicate 2 scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136771", "GSM8136771: GC122775  HuNoV infected  replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM8136771 r1", "GSM8136771", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz", "fastq fastq", 6313572727.0, 53055233.0, "GSM8136771 r2", "0:28 1:91", "A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282", 28, 91, null, null, 1709609257, 1491468410, 1640296277, 1472111501, 87282, "SRX23882001", "SRS20705714", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30696, "SRR28272068", "SRX23882000", "SRS20705713", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122774  HuNoV infected  replicate 1  scRNAseq", "GSM8136770", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122774  HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136770", "GSM8136770: GC122774  HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136770 r1", "GSM8136770", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz", "fastq fastq", 15738518978.0, 132256462.0, "GSM8136770 r1", "0:28 1:91", "A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212", 28, 91, null, null, 4181691582, 3761213961, 4083789142, 3711597081, 227212, "SRX23882000", "SRS20705713", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30697, "SRR28272069", "SRX23882000", "SRS20705713", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122774  HuNoV infected  replicate 1  scRNAseq", "GSM8136770", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122774  HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136770", "GSM8136770: GC122774  HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136770 r1", "GSM8136770", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz", "fastq fastq", 15261653253.0, 128249187.0, "GSM8136770 r2", "0:28 1:91", "A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693", 28, 91, null, null, 4059552936, 3644406570, 3954261902, 3603216152, 215693, "SRX23882000", "SRS20705713", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30698, "SRR28272070", "SRX23881999", "SRS20705712", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122773  uninfected  replicate 2  scRNAseq", "GSM8136769", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122773  uninfected  replicate 2  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136769", "GSM8136769: GC122773  uninfected  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM8136769 r1", "GSM8136769", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz", "fastq fastq", 15150656598.0, 127316442.0, "GSM8136769 r1", "0:28 1:91", "A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113", 28, 91, null, null, 4100783574, 3526779401, 3845684506, 3677189004, 220113, "SRX23881999", "SRS20705712", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30699, "SRR28272071", "SRX23881999", "SRS20705712", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122773  uninfected  replicate 2  scRNAseq", "GSM8136769", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122773  uninfected  replicate 2  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136769", "GSM8136769: GC122773  uninfected  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM8136769 r1", "GSM8136769", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz", "fastq fastq", 14942015326.0, 125563154.0, "GSM8136769 r2", "0:28 1:91", "A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808", 28, 91, null, null, 4048600218, 3475105088, 3787275869, 3630822343, 211808, "SRX23881999", "SRS20705712", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30700, "SRR28272072", "SRX23881998", "SRS20705711", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122772  uninfected  replicate 1  scRNAseq", "GSM8136768", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122772  uninfected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136768", "GSM8136768: GC122772  uninfected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136768 r1", "GSM8136768", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz", "fastq fastq", 7397061301.0, 62160179.0, "GSM8136768 r1", "0:28 1:91", "A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806", 28, 91, null, null, 2023651844, 1711760729, 1860691426, 1800850496, 106806, "SRX23881998", "SRS20705711", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30701, "SRR28272073", "SRX23881998", "SRS20705711", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122772  uninfected  replicate 1  scRNAseq", "GSM8136768", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122772  uninfected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136768", "GSM8136768: GC122772  uninfected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136768 r1", "GSM8136768", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz", "fastq fastq", 7290496444.0, 61264676.0, "GSM8136768 r2", "0:28 1:91", "A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196", 28, 91, null, null, 1996736343, 1685693360, 1830823892, 1777138653, 104196, "SRX23881998", "SRS20705711", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [33014, "SRR29633212", "SRX25139207", "SRS21831220", "SRP516661", "PRJNA1129181", "A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing", "GSE271002", "Transcriptome Analysis", "To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.", null, "pubmed:40252728", null, "Mtz  5dpf", "GSM8366963", null, "source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing", "Mtz  5dpf", "Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files", "Dissected larval intestines", null, "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole", "GSM8366963", "GSM8366963: Mtz  5dpf; Danio rerio; RNA Seq", "GSM8366963 r1", "GSM8366963", "1", "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP516661", null, "loader:fastq load.py", "NTR-Mtz-d5_R1.fastq.gz NTR-Mtz-d5_R2.fastq.gz", "fastq fastq", 105173263361.0, 348971465.0, "GSM8366963 r1", "0:150.76 1:150.62", "A:29260313483;C:18342577741;G:20471735616;T:37097033318;N:1603203", 150, 150, null, null, 29260313483, 18342577741, 20471735616, 37097033318, 1603203, "SRX25139207", "SRS21831220", "SRA1911905", "Karolinska Institutet", "Karolinska Institutet", 2, 0.56019, 0.89517, 0.13273, 0.11945, 0.9795, 0.82258, 0.63676, 0.6161, 151, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-06-27", "Larval", "Larval", "Gut", "Digestive System"], [33015, "SRR29633213", "SRX25139206", "SRS21831219", "SRP516661", "PRJNA1129181", "A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing", "GSE271002", "Transcriptome Analysis", "To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.", null, "pubmed:40252728", null, "Control  5dpf", "GSM8366962", null, "source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing", "Control  5dpf", "Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files", "Dissected larval intestines", null, "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control", "GSM8366962", "GSM8366962: Control  5dpf; Danio rerio; RNA Seq", "GSM8366962 r1", "GSM8366962", "1", "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP516661", null, "loader:fastq load.py", "NTR-Control-d5_R1.fastq.gz NTR-Control-d5_R2.fastq.gz", "fastq fastq", 139967773505.0, 464402100.0, "GSM8366962 r1", "0:150.76 1:150.63", "A:39202616731;C:24289494719;G:27175225437;T:49298534102;N:1902516", 150, 150, null, null, 39202616731, 24289494719, 27175225437, 49298534102, 1902516, "SRX25139206", "SRS21831219", "SRA1911905", "Karolinska Institutet", "Karolinska Institutet", 2, 0.54902, 0.89315, 0.13449, 0.13341, 0.97954, 0.80553, 0.69256, 0.59244, 151, 151, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-06-27", "Larval", "Larval", "Gut", "Digestive System"], [33016, "SRR29633214", "SRX25139205", "SRS21831218", "SRP516661", "PRJNA1129181", "A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing", "GSE271002", "Transcriptome Analysis", "To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.", null, "pubmed:40252728", null, "Mtz  ablation 4dpf", "GSM8366961", null, "source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing", "Mtz  ablation 4dpf", "Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files", "Dissected larval intestines", null, "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole", "GSM8366961", "GSM8366961: Mtz  ablation 4dpf; Danio rerio; RNA Seq", "GSM8366961 r1", "GSM8366961", "1", "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP516661", null, "loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R1 001.fastq.gz   read2PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R2 001.fastq.gz   read3PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I1 001.fastq.gz   read4PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I2 001.fastq.gz", "Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R1_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I1_001.fastq.gz", "fastq fastq fastq fastq", 33049837760.0, 103280743.0, "GSM8366961 r1", "0:150 1:150 2:10 3:10", "A:9739096160;C:6338831532;G:6106096444;T:8799858219;N:340545", 150, 150, 10, 10, 9739096160, 6338831532, 6106096444, 8799858219, 340545, "SRX25139205", "SRS21831218", "SRA1911905", "Karolinska Institutet", "Karolinska Institutet", 2, 0.0, 0.91169, 0.0, 0.19328, 1.0, 0.81722, null, 0.64993, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-06-27", "Larval", "Larval", "Gut", "Digestive System"], [33017, "SRR29633215", "SRX25139204", "SRS21831217", "SRP516661", "PRJNA1129181", "A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing", "GSE271002", "Transcriptome Analysis", "To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.", null, "pubmed:40252728", null, "Control  ablation 4dpf", "GSM8366960", null, "source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing", "Control  ablation 4dpf", "Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files", "Dissected larval intestines", null, "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control", "GSM8366960", "GSM8366960: Control  ablation 4dpf; Danio rerio; RNA Seq", "GSM8366960 r1", "GSM8366960", "1", "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP516661", null, "loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz   read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz   read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz   read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz", "Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz", "fastq fastq fastq fastq", 115286504000.0, 360270325.0, "GSM8366960 r1", "0:150 1:150 2:10 3:10", "A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542", 150, 150, 10, 10, 32679027944, 17748865933, 17885040590, 39764959491, 3203542, "SRX25139204", "SRS21831217", "SRA1911905", "Karolinska Institutet", "Karolinska Institutet", 2, 0.39015, 0.90036, 0.10989, 0.19421, 0.97845, 0.79401, 0.69547, 0.6103, 150, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-06-27", "Larval", "Larval", "Gut", "Digestive System"], [33417, "SRR30186672", "SRX25652379", "SRS22295184", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS6dpf", "GSM8448586", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing", "ENS6dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf", "GSM8448586", "GSM8448586: ENS6dpf; Danio rerio; RNA Seq", "GSM8448586 r1", "GSM8448586", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26637_S5_L005_I1_001.fastq.gz FT-SA26637_S5_L005_R1_001.fastq.gz FT-SA26637_S5_L005_R2_001.fastq.gz", "fastq fastq fastq", 40502433410.0, 130653011.0, "GSM8448586 r1", "0:8 1:151 2:151", "A:10014178947;C:5704376875;G:6596271508;T:17137143949;N:5238043", 8, 151, 151, null, 10014178947, 5704376875, 6596271508, 17137143949, 5238043, "SRX25652379", "SRS22295184", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33418, "SRR30186673", "SRX25652379", "SRS22295184", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS6dpf", "GSM8448586", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing", "ENS6dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf", "GSM8448586", "GSM8448586: ENS6dpf; Danio rerio; RNA Seq", "GSM8448586 r1", "GSM8448586", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26637_S5_L006_I1_001.fastq.gz FT-SA26637_S5_L006_R1_001.fastq.gz FT-SA26637_S5_L006_R2_001.fastq.gz", "fastq fastq fastq", 41972742020.0, 135395942.0, "GSM8448586 r2", "0:8 1:151 2:151", "A:10346550415;C:6105559893;G:6757897068;T:17672755179;N:6811929", 8, 151, 151, null, 10346550415, 6105559893, 6757897068, 17672755179, 6811929, "SRX25652379", "SRS22295184", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33419, "SRR30186674", "SRX25652378", "SRS22295179", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS5dpf", "GSM8448585", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing", "ENS5dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf", "GSM8448585", "GSM8448585: ENS5dpf; Danio rerio; RNA Seq", "GSM8448585 r1", "GSM8448585", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26636_S4_L005_I1_001.fastq.gz FT-SA26636_S4_L005_R1_001.fastq.gz FT-SA26636_S4_L005_R2_001.fastq.gz", "fastq fastq fastq", 21590505830.0, 69646793.0, "GSM8448585 r1", "0:8 1:151 2:151", "A:5324745627;C:3047288539;G:3517496789;T:9140955618;N:2844913", 8, 151, 151, null, 5324745627, 3047288539, 3517496789, 9140955618, 2844913, "SRX25652378", "SRS22295179", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33420, "SRR30186675", "SRX25652378", "SRS22295179", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS5dpf", "GSM8448585", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing", "ENS5dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf", "GSM8448585", "GSM8448585: ENS5dpf; Danio rerio; RNA Seq", "GSM8448585 r1", "GSM8448585", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26636_S4_L006_I1_001.fastq.gz FT-SA26636_S4_L006_R1_001.fastq.gz FT-SA26636_S4_L006_R2_001.fastq.gz", "fastq fastq fastq", 22493595040.0, 72559984.0, "GSM8448585 r2", "0:8 1:151 2:151", "A:5532271824;C:3275587569;G:3623404196;T:9478183540;N:3668039", 8, 151, 151, null, 5532271824, 3275587569, 3623404196, 9478183540, 3668039, "SRX25652378", "SRS22295179", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33421, "SRR30186676", "SRX25652377", "SRS22295180", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS4dpf", "GSM8448584", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing", "ENS4dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf", "GSM8448584", "GSM8448584: ENS4dpf; Danio rerio; RNA Seq", "GSM8448584 r1", "GSM8448584", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26635_S3_L005_I1_001.fastq.gz FT-SA26635_S3_L005_R1_001.fastq.gz FT-SA26635_S3_L005_R2_001.fastq.gz", "fastq fastq fastq", 29011782450.0, 93586395.0, "GSM8448584 r1", "0:8 1:151 2:151", "A:7041483148;C:4220842692;G:4903817651;T:12093250712;N:3697087", 8, 151, 151, null, 7041483148, 4220842692, 4903817651, 12093250712, 3697087, "SRX25652377", "SRS22295180", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33422, "SRR30186677", "SRX25652377", "SRS22295180", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS4dpf", "GSM8448584", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing", "ENS4dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf", "GSM8448584", "GSM8448584: ENS4dpf; Danio rerio; RNA Seq", "GSM8448584 r1", "GSM8448584", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26635_S3_L006_I1_001.fastq.gz FT-SA26635_S3_L006_R1_001.fastq.gz FT-SA26635_S3_L006_R2_001.fastq.gz", "fastq fastq fastq", 30061975960.0, 96974116.0, "GSM8448584 r2", "0:8 1:151 2:151", "A:7272472037;C:4518131790;G:5023942263;T:12466801069;N:4835873", 8, 151, 151, null, 7272472037, 4518131790, 5023942263, 12466801069, 4835873, "SRX25652377", "SRS22295180", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33423, "SRR30186678", "SRX25652376", "SRS22295175", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS3dpf", "GSM8448583", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing", "ENS3dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf", "GSM8448583", "GSM8448583: ENS3dpf; Danio rerio; RNA Seq", "GSM8448583 r1", "GSM8448583", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26634_S2_L005_I1_001.fastq.gz FT-SA26634_S2_L005_R1_001.fastq.gz FT-SA26634_S2_L005_R2_001.fastq.gz", "fastq fastq fastq", 28701845380.0, 92586598.0, "GSM8448583 r1", "0:8 1:151 2:151", "A:6898569356;C:4281479855;G:4993869601;T:11783488306;N:3745478", 8, 151, 151, null, 6898569356, 4281479855, 4993869601, 11783488306, 3745478, "SRX25652376", "SRS22295175", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [33424, "SRR30186679", "SRX25652376", "SRS22295175", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS3dpf", "GSM8448583", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing", "ENS3dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf", "GSM8448583", "GSM8448583: ENS3dpf; Danio rerio; RNA Seq", "GSM8448583 r1", "GSM8448583", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26634_S2_L006_I1_001.fastq.gz FT-SA26634_S2_L006_R1_001.fastq.gz FT-SA26634_S2_L006_R2_001.fastq.gz", "fastq fastq fastq", 29814490250.0, 96175775.0, "GSM8448583 r2", "0:8 1:151 2:151", "A:7143218463;C:4592538828;G:5130593993;T:12173956857;N:4775909", 8, 151, 151, null, 7143218463, 4592538828, 5130593993, 12173956857, 4775909, "SRX25652376", "SRS22295175", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "Larval", "Larval", "Gut", "Digestive System"], [34137, "SRR31360761", "SRX26734629", "SRS23224778", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "WT3", null, "strain:AB|isolate:WT3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "WT3.fq", "WT3.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "WT3_R1.fq.gz WT3_R2.fq.gz", "fastq fastq", 7045875300.0, 23486251.0, "WT3 R1.fq.gz", "0:150 1:150", "A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080", 150, 150, null, null, 1817741681, 1708030651, 1712073267, 1808003621, 26080, "SRX26734629", "SRS23224778", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34138, "SRR31360762", "SRX26734628", "SRS23224777", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "WT2", null, "strain:AB|isolate:WT2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "WT2.fq", "WT2.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "WT2_R1.fq.gz WT2_R2.fq.gz", "fastq fastq", 6888570900.0, 22961903.0, "WT2 R1.fq.gz", "0:150 1:150", "A:1774584110;C:1673773734;G:1678866397;T:1761321702;N:24957", 150, 150, null, null, 1774584110, 1673773734, 1678866397, 1761321702, 24957, "SRX26734628", "SRS23224777", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34139, "SRR31360763", "SRX26734627", "SRS23224776", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "WT1", null, "strain:AB|isolate:WT1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "WT1.fq", "WT1.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "WT1_R1.fq.gz WT1_R2.fq.gz", "fastq fastq", 6815123400.0, 22717078.0, "WT1 R1.fq.gz", "0:150 1:150", "A:1758536338;C:1650339290;G:1657619698;T:1748603714;N:24360", 150, 150, null, null, 1758536338, 1650339290, 1657619698, 1748603714, 24360, "SRX26734627", "SRS23224776", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34140, "SRR31360764", "SRX26734626", "SRS23224775", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "mu3", null, "strain:AB|isolate:mu3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "mu3.fq", "mu3.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "mu3_R1.fq.gz mu3_R2.fq.gz", "fastq fastq", 7304650200.0, 24348834.0, "mu3 R1.fq.gz", "0:150 1:150", "A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419", 150, 150, null, null, 1934717193, 1720864609, 1730177787, 1918863192, 27419, "SRX26734626", "SRS23224775", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34141, "SRR31360765", "SRX26734625", "SRS23224774", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "mu2", null, "strain:AB|isolate:mu2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "mu2.fq", "mu2.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "mu2_R1.fq.gz mu2_R2.fq.gz", "fastq fastq", 7168114200.0, 23893714.0, "mu2 R1.fq.gz", "0:150 1:150", "A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459", 150, 150, null, null, 1896004564, 1692025000, 1701080897, 1878977280, 26459, "SRX26734625", "SRS23224774", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [34142, "SRR31360766", "SRX26734624", "SRS23224773", "SRP545397", "PRJNA1186411", "Zebrafish intestine sequencing", "PRJNA1186411", "Other", "To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions", null, null, null, null, "mu1", null, "strain:AB|isolate:mu1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larvae intestine", "mu1.fq", "mu1.fq", "nomal RAN Seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP545397", null, null, "mu1_R1.fq.gz mu1_R2.fq.gz", "fastq fastq", 7262664600.0, 24208882.0, "mu1 R1.fq.gz", "0:150 1:150", "A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590", 150, 150, null, null, 1922666653, 1711620445, 1720530432, 1907824480, 22590, "SRX26734624", "SRS23224773", "SRA2015506", "Fudan University|School of Life Sciences", "Fudan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-11-15", "Larval", "Larval", "Gut", "Digestive System"], [41072, "SRR3655801", "SRX1836012", "SRS1495476", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "GSM2195935", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195935", "GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq", "GSM2195935", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS410.fastq.gz", "fastq", 1402184556.0, 18692635.0, "GSM2195935 r1", "0:75.01 1:0", "A:363262740;C:326626075;G:322630446;T:389582075;N:83220", 75, 0, null, null, 363262740, 326626075, 322630446, 389582075, 83220, "SRX1836012", "SRS1495476", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92115, null, 0.08008, null, 0.7389, null, 0.52691, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41073, "SRR3655802", "SRX1836012", "SRS1495476", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "GSM2195935", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195935", "GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq", "GSM2195935", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS410.fastq.gz", "fastq", 3450884531.0, 46005067.0, "GSM2195935 r2", "0:75.01 1:0", "A:874448337;C:808236306;G:797225707;T:970673048;N:301133", 75, 0, null, null, 874448337, 808236306, 797225707, 970673048, 301133, "SRX1836012", "SRS1495476", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.93035, null, 0.08192, null, 0.73271, null, 0.52273, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41074, "SRR3655799", "SRX1836011", "SRS1495475", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "GSM2195934", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195934", "GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq", "GSM2195934", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195934", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS409.fastq.gz", "fastq", 1422635421.0, 18963577.0, "GSM2195934 r1", "0:75.02 1:0", "A:362173330;C:332883466;G:329078937;T:398420070;N:79618", 75, 0, null, null, 362173330, 332883466, 329078937, 398420070, 79618, "SRX1836011", "SRS1495475", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92474, null, 0.07466, null, 0.73423, null, 0.50871, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41075, "SRR3655800", "SRX1836011", "SRS1495475", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "GSM2195934", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195934", "GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq", "GSM2195934", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195934", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS409.fastq.gz", "fastq", 3549432159.0, 47315580.0, "GSM2195934 r2", "0:75.02 1:0", "A:893492844;C:832741437;G:822208498;T:1000698758;N:290622", 75, 0, null, null, 893492844, 832741437, 822208498, 1000698758, 290622, "SRX1836011", "SRS1495475", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.93197, null, 0.07554, null, 0.73109, null, 0.50825, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41076, "SRR3655797", "SRX1836010", "SRS1495474", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "GSM2195933", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195933", "GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq", "GSM2195933", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195933", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS408.fastq.gz", "fastq", 1400640841.0, 18670640.0, "GSM2195933 r1", "0:75.02 1:0", "A:363544908;C:324586412;G:320620988;T:391797091;N:91442", 75, 0, null, null, 363544908, 324586412, 320620988, 391797091, 91442, "SRX1836010", "SRS1495474", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92971, null, 0.10926, null, 0.73016, null, 0.51418, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41077, "SRR3655798", "SRX1836010", "SRS1495474", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "GSM2195933", null, "tissue:full thickness intestine|status:SBS", "Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SBS", "GSM2195933", "GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq", "GSM2195933", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195933", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS408.fastq.gz", "fastq", 1400640841.0, 18670640.0, "GSM2195933 r2", "0:75.02 1:0", "A:363544908;C:324586412;G:320620988;T:391797091;N:91442", 75, 0, null, null, 363544908, 324586412, 320620988, 391797091, 91442, "SRX1836010", "SRS1495474", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92977, null, 0.10933, null, 0.73008, null, 0.51355, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Larval", "Larval", "Gut", "Digestive System"], [41575, "SRR5045902", "SRX2368488", "SRS1814332", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutCV 2", "GSM2401374", null, "source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutCV 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401374", "GSM2401374: MutCV 2; Danio rerio; RNA Seq", "GSM2401374", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401374", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutCV_2.fastq", "fastq", 3876906576.0, 76017776.0, "GSM2401374 r1", "0:51 1:0", "A:957781980;C:915286453;G:859927041;T:1143804372;N:106730", 51, 0, null, null, 957781980, 915286453, 859927041, 1143804372, 106730, "SRX2368488", "SRS1814332", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96196, null, 0.11375, null, 0.70887, null, 0.53406, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41576, "SRR5045901", "SRX2368487", "SRS1814330", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutCV 1", "GSM2401373", null, "source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutCV 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401373", "GSM2401373: MutCV 1; Danio rerio; RNA Seq", "GSM2401373", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401373", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutCV_1.fastq", "fastq", 3835824444.0, 75212244.0, "GSM2401373 r1", "0:51 1:0", "A:946407906;C:904393791;G:851683286;T:1133241327;N:98134", 51, 0, null, null, 946407906, 904393791, 851683286, 1133241327, 98134, "SRX2368487", "SRS1814330", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.95795, null, 0.11761, null, 0.70481, null, 0.53357, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41577, "SRR5045900", "SRX2368486", "SRS1814331", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutGF 2", "GSM2401372", null, "source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutGF 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401372", "GSM2401372: MutGF 2; Danio rerio; RNA Seq", "GSM2401372", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401372", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutGF_2.fastq", "fastq", 3299677866.0, 64699566.0, "GSM2401372 r1", "0:51 1:0", "A:809247440;C:784035543;G:731742820;T:974610541;N:41522", 51, 0, null, null, 809247440, 784035543, 731742820, 974610541, 41522, "SRX2368486", "SRS1814331", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96247, null, 0.1049, null, 0.74034, null, 0.5525, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41578, "SRR5045899", "SRX2368485", "SRS1814329", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "MutGF 1", "GSM2401371", null, "source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "MutGF 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract", "GSM2401371", "GSM2401371: MutGF 1; Danio rerio; RNA Seq", "GSM2401371", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401371", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "MutGF_1.fastq", "fastq", 3734921199.0, 73233749.0, "GSM2401371 r1", "0:51 1:0", "A:923493830;C:879193170;G:840678282;T:1091454504;N:101413", 51, 0, null, null, 923493830, 879193170, 840678282, 1091454504, 101413, "SRX2368485", "SRS1814329", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96328, null, 0.1099, null, 0.73492, null, 0.50455, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41579, "SRR5045898", "SRX2368484", "SRS1814328", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTCV 3", "GSM2401370", null, "source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTCV 3", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401370", "GSM2401370: WTCV 3; Danio rerio; RNA Seq", "GSM2401370", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401370", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTCV_3.fastq", "fastq", 3928418412.0, 77027812.0, "GSM2401370 r1", "0:51 1:0", "A:966197912;C:939595492;G:912123411;T:1110393846;N:107751", 51, 0, null, null, 966197912, 939595492, 912123411, 1110393846, 107751, "SRX2368484", "SRS1814328", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97188, null, 0.08862, null, 0.7357, null, 0.53339, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41580, "SRR5045897", "SRX2368483", "SRS1814327", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTCV 2", "GSM2401369", null, "source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTCV 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401369", "GSM2401369: WTCV 2; Danio rerio; RNA Seq", "GSM2401369", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401369", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTCV_2.fastq", "fastq", 3782941473.0, 74175323.0, "GSM2401369 r1", "0:51 1:0", "A:928563733;C:910471684;G:872137892;T:1071716851;N:51313", 51, 0, null, null, 928563733, 910471684, 872137892, 1071716851, 51313, "SRX2368483", "SRS1814327", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97097, null, 0.09668, null, 0.74255, null, 0.55455, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41581, "SRR5045896", "SRX2368482", "SRS1814326", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTCV 1", "GSM2401368", null, "source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTCV 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401368", "GSM2401368: WTCV 1; Danio rerio; RNA Seq", "GSM2401368", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTCV_1.fastq", "fastq", 3643146954.0, 71434254.0, "GSM2401368 r1", "0:51 1:0", "A:877377891;C:875020597;G:839793450;T:1050862579;N:92437", 51, 0, null, null, 877377891, 875020597, 839793450, 1050862579, 92437, "SRX2368482", "SRS1814326", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.9683, null, 0.08514, null, 0.73525, null, 0.55486, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41582, "SRR5045895", "SRX2368481", "SRS1814325", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTGF 3", "GSM2401367", null, "source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTGF 3", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401367", "GSM2401367: WTGF 3; Danio rerio; RNA Seq", "GSM2401367", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401367", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTGF_3.fastq", "fastq", 3462802386.0, 67898086.0, "GSM2401367 r1", "0:51 1:0", "A:843407439;C:830117704;G:803633976;T:985548502;N:94765", 51, 0, null, null, 843407439, 830117704, 803633976, 985548502, 94765, "SRX2368481", "SRS1814325", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97202, null, 0.08623, null, 0.75939, null, 0.56558, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41583, "SRR5045894", "SRX2368480", "SRS1814324", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTGF 2", "GSM2401366", null, "source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTGF 2", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401366", "GSM2401366: WTGF 2; Danio rerio; RNA Seq", "GSM2401366", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401366", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTGF_2.fastq", "fastq", 3699149799.0, 72532349.0, "GSM2401366 r1", "0:51 1:0", "A:907425678;C:884609705;G:855651232;T:1051368070;N:95114", 51, 0, null, null, 907425678, 884609705, 855651232, 1051368070, 95114, "SRX2368480", "SRS1814324", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.96861, null, 0.08856, null, 0.75223, null, 0.55327, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [41584, "SRR5045893", "SRX2368479", "SRS1814323", "SRP093775", "PRJNA354631", "Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq", "GSE90446", "Transcriptome Analysis", "We performed RNA seq from 6 dpf hnf4a /  and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free  GF or presence Conventionalized  CV of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes  indicating that the microbiota supress Hnf4a trans activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a /  and hnf4a+/+ zebrafish larvae in the absence Germ Free  GF or presence Conventionalized  CV microbiota.", "parent bioproject:PRJNA354702", "pubmed:28385711", null, "WTGF 1", "GSM2401365", null, "source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "WTGF 1", "Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig", "zebrafish digestive tracts", "Lines were maintained on a TL/T\u00fc background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield  2000. Production  colonization  maintenance  and sterility testing of gnotobiotic zebrafish were performed as described Pham et al.  2008.", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", null, "condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract", "GSM2401365", "GSM2401365: WTGF 1; Danio rerio; RNA Seq", "GSM2401365", null, "1", "Zebrafish digestive tracts n = 13 \u2013 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026.  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4\u00b0C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination.  RNA was eluted off the column in nuclease free water  quantified using a Qubit 2.0 and stored at  80\u00b0C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.", "GEO Accession:GSM2401365", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP093775", null, null, "WTGF_1.fastq", "fastq", 3948593247.0, 77423397.0, "GSM2401365 r1", "0:51 1:0", "A:951060123;C:949871425;G:909862458;T:1137745436;N:53805", 51, 0, null, null, 951060123, 949871425, 909862458, 1137745436, 53805, "SRX2368479", "SRS1814323", "SRA497672", "GEO", "Duke University School of Medicine", 1, 0.97252, null, 0.08483, null, 0.74418, null, 0.54605, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-11-22", "Larval", "Larval", "Gut", "Digestive System"], [44033, "SRR6231893", "SRX3340325", "SRS2641976", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP positive cells", "en GFP positive JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP positive JK r1", "en GFP positive JK r1 fwd", "en GFP positive JK r1 fwd", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFPA_GCCAAT_R1_001.fastq.gz d7phoGFPA_GCCAAT_R2_001.fastq.gz", "fastq fastq", 22618935400.0, 113094677.0, "d7phoGFPA GCCAAT R1 001.fastq.gz", "0:100 1:100", "A:6233619158;C:5097706589;G:5045972110;T:6222785585;N:18851958", 100, 100, null, null, 6233619158, 5097706589, 5045972110, 6222785585, 18851958, "SRX3340325", "SRS2641976", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.91266, 0.9056, 0.16638, 0.16643, 0.68008, 0.68367, 0.48483, 0.48254, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-10-27", "Larval", "Larval", "Gut", "Digestive System"], [44034, "SRR6231894", "SRX3340324", "SRS2641976", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP positive cells", "en GFP positive JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP positive JK r2", "en GFP positive JK r2 fwd", "en GFP positive JK r2 fwd", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFPB_GTGAAA_R2_001.fastq.gz d7phoGFPB_GTGAAA_R1_001.fastq.gz", "fastq fastq", 13753541400.0, 68767707.0, "d7phoGFPB GTGAAA R1 001.fastq.gz", "0:100 1:100", "A:3807602619;C:3077358417;G:3063510819;T:3793560543;N:11509002", 100, 100, null, null, 3807602619, 3077358417, 3063510819, 3793560543, 11509002, "SRX3340324", "SRS2641976", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.90465, 0.89478, 0.20689, 0.2048, 0.68402, 0.68738, 0.4887, 0.48279, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-10-27", "Larval", "Larval", "Gut", "Digestive System"], [44035, "SRR6231895", "SRX3340323", "SRS2641979", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP negative cells", "en GFP negative JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal non neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP negative JK r1", "en GFP negative JK r1 fwd", "en GFP negative JK r1 fwd", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFP-A_ACAGTG_R1_001.fastq.gz d7phoGFP-A_ACAGTG_R2_001.fastq.gz", "fastq fastq", 17591029600.0, 87955148.0, "d7phoGFP A ACAGTG R2 001.fastq.gz", "0:100 1:100", "A:4757105599;C:4046056704;G:4012427038;T:4760767597;N:14672662", 100, 100, null, null, 4757105599, 4046056704, 4012427038, 4760767597, 14672662, "SRX3340323", "SRS2641979", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.91795, 0.92394, 0.12634, 0.12565, 0.69479, 0.68976, 0.50879, 0.5095, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-10-27", "Larval", "Larval", "Gut", "Digestive System"], [44036, "SRR6231897", "SRX3340321", "SRS2641979", "SRP122541", "PRJNA415856", "Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment", "PRJNA415856", "Transcriptome Analysis", "Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.", null, "pubmed:28403821", null, "GFP negative cells", "en GFP negative JK", null, "strain:phox2b Tgphox2b:EGFP w37|dev stage:7 dpf male and female|tissue:Intestine|biomaterial provider:Kuhlman lab|cell type:Intestinal non neurons|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "en GFP negative JK r2", "en GFP negative JK r2 rev", "en GFP negative JK r2 rev", "The library was prepapred by the Iowa State DNA facility.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP122541", null, null, "d7phoGFP-B_CTTGTA_R1_001.fastq.gz d7phoGFP-B_CTTGTA_R2_001.fastq.gz", "fastq fastq", 21627852000.0, 108139260.0, "d7phoGFP B CTTGTA R2 001.fastq.gz", "0:100 1:100", "A:5802401896;C:5026391965;G:4975450919;T:5805553498;N:18053722", 100, 100, null, null, 5802401896, 5026391965, 4975450919, 5805553498, 18053722, "SRX3340321", "SRS2641979", "SRA625723", "Iowa State University|Genetics Development and Cell Biology", "Iowa State University", 2, 0.93032, 0.9242, 0.11858, 0.1194, 0.69209, 0.69544, 0.50104, 0.50121, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-02", "Larval", "Larval", "Gut", "Digestive System"], [49070, "SRR7641841", "SRX4505270", "SRS3625663", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 9dpf wt3", "GSM3318287", null, "source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 9dpf wt3", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318287", "GSM3318287: Danio rerio RNAseq intestine 9dpf wt3; Danio rerio; RNA Seq", "GSM3318287", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318287", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt9dpf3_AGTCAA_R2.fastq.gz lane1_BSwt9dpf3_AGTCAA_R1.fastq.gz", "fastq fastq", 2761029656.0, 32104996.0, "GSM3318287 r1", "0:43 1:43", "A:708766648;C:643915678;G:711330854;T:696326829;N:689647", 43, 43, null, null, 708766648, 643915678, 711330854, 696326829, 689647, "SRX4505270", "SRS3625663", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.89599, 0.88107, 0.38979, 0.37161, 0.72523, 0.72705, 0.60581, 0.60845, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49071, "SRR7641840", "SRX4505269", "SRS3625661", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 9dpf wt2", "GSM3318286", null, "source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 9dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318286", "GSM3318286: Danio rerio RNAseq intestine 9dpf wt2; Danio rerio; RNA Seq", "GSM3318286", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318286", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt9dpf2_GGCTAC_R2.fastq.gz lane1_BSwt9dpf2_GGCTAC_R1.fastq.gz", "fastq fastq", 3774884086.0, 43894001.0, "GSM3318286 r1", "0:43 1:43", "A:912580559;C:950011527;G:1000247169;T:911105213;N:939618", 43, 43, null, null, 912580559, 950011527, 1000247169, 911105213, 939618, "SRX4505269", "SRS3625661", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.91348, 0.89692, 0.32028, 0.31, 0.75479, 0.76398, 0.64335, 0.62378, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49072, "SRR7641838", "SRX4505267", "SRS3625659", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 9dpf wt1", "GSM3318285", null, "source name:intestine|strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 9dpf wt1", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:9 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318285", "GSM3318285: Danio rerio RNAseq intestine 9dpf wt1; Danio rerio; RNA Seq", "GSM3318285", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318285", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt9dpf1_TAGCTT_R2.fastq.gz lane1_BSwt9dpf1_TAGCTT_R1.fastq.gz", "fastq fastq", 2839107938.0, 33012883.0, "GSM3318285 r1", "0:43 1:43", "A:706052485;C:678593541;G:744406061;T:709347067;N:708784", 43, 43, null, null, 706052485, 678593541, 744406061, 709347067, 708784, "SRX4505267", "SRS3625659", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.90142, 0.89053, 0.40928, 0.39461, 0.72622, 0.72768, 0.51721, 0.5385, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49073, "SRR7641837", "SRX4505266", "SRS3625658", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 7dpf wt3", "GSM3318284", null, "source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 7dpf wt3", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318284", "GSM3318284: Danio rerio RNAseq intestine 7dpf wt3; Danio rerio; RNA Seq", "GSM3318284", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318284", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt7dpf3_GATCAG_R1.fastq.gz lane1_BSwt7dpf3_GATCAG_R2.fastq.gz", "fastq fastq", 3032189462.0, 35258017.0, "GSM3318284 r1", "0:43 1:43", "A:728621779;C:727851984;G:867302660;T:707649251;N:763788", 43, 43, null, null, 728621779, 727851984, 867302660, 707649251, 763788, "SRX4505266", "SRS3625658", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.87964, 0.8732, 0.36258, 0.35306, 0.7259, 0.72934, 0.56793, 0.56457, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49074, "SRR7641836", "SRX4505265", "SRS3625657", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 7dpf wt2", "GSM3318283", null, "source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 7dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318283", "GSM3318283: Danio rerio RNAseq intestine 7dpf wt2; Danio rerio; RNA Seq", "GSM3318283", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318283", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt7dpf2_ACTTGA_R2.fastq.gz lane1_BSwt7dpf2_ACTTGA_R1.fastq.gz", "fastq fastq", 2796267812.0, 32514742.0, "GSM3318283 r1", "0:43 1:43", "A:678627733;C:682194336;G:763077086;T:671672090;N:696567", 43, 43, null, null, 678627733, 682194336, 763077086, 671672090, 696567, "SRX4505265", "SRS3625657", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.88818, 0.88174, 0.43784, 0.42578, 0.72531, 0.72417, 0.51845, 0.53225, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49075, "SRR7641834", "SRX4505264", "SRS3625656", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 7dpf wt1", "GSM3318282", null, "source name:intestine|strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 7dpf wt1", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:7 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318282", "GSM3318282: Danio rerio RNAseq intestine 7dpf wt1; Danio rerio; RNA Seq", "GSM3318282", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318282", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt7dpf1_TTAGGC_R2.fastq.gz lane1_BSwt7dpf1_TTAGGC_R1.fastq.gz", "fastq fastq", 2657998302.0, 30906957.0, "GSM3318282 r1", "0:43 1:43", "A:670335271;C:630669243;G:685436534;T:670905092;N:652162", 43, 43, null, null, 670335271, 630669243, 685436534, 670905092, 652162, "SRX4505264", "SRS3625656", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.87993, 0.87022, 0.42578, 0.40713, 0.69828, 0.70244, 0.54254, 0.55209, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49076, "SRR7641833", "SRX4505263", "SRS3625655", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt3", "GSM3318281", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt3", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318281", "GSM3318281: Danio rerio RNAseq intestine 5dpf wt3; Danio rerio; RNA Seq", "GSM3318281", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318281", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf3_CAGATC_R1.fastq.gz lane1_BSwt5dpf3_CAGATC_R2.fastq.gz", "fastq fastq", 3471426378.0, 40365423.0, "GSM3318281 r1", "0:43 1:43", "A:816007186;C:888388842;G:957708559;T:808447064;N:874727", 43, 43, null, null, 816007186, 888388842, 957708559, 808447064, 874727, "SRX4505263", "SRS3625655", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.86569, 0.86483, 0.38669, 0.37568, 0.7277, 0.73148, 0.51986, 0.52105, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49077, "SRR7641832", "SRX4505262", "SRS3625654", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt2", "GSM3318280", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318280", "GSM3318280: Danio rerio RNAseq intestine 5dpf wt2; Danio rerio; RNA Seq", "GSM3318280", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318280", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf2_GCCAAT_R2.fastq.gz lane1_BSwt5dpf2_GCCAAT_R1.fastq.gz", "fastq fastq", 2424100404.0, 28187214.0, "GSM3318280 r1", "0:43 1:43", "A:657799034;C:534330605;G:575770800;T:655604713;N:595252", 43, 43, null, null, 657799034, 534330605, 575770800, 655604713, 595252, "SRX4505262", "SRS3625654", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.85487, 0.83514, 0.56287, 0.53286, 0.69583, 0.69658, 0.54518, 0.55246, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [49078, "SRR7641830", "SRX4505261", "SRS3625653", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt1", "GSM3318279", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt1", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318279", "GSM3318279: Danio rerio RNAseq intestine 5dpf wt1; Danio rerio; RNA Seq", "GSM3318279", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318279", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf1_ACAGTG_R1.fastq.gz lane1_BSwt5dpf1_ACAGTG_R2.fastq.gz", "fastq fastq", 2258154890.0, 26257615.0, "GSM3318279 r1", "0:43 1:43", "A:568380294;C:542047927;G:584939179;T:562222871;N:564619", 43, 43, null, null, 568380294, 542047927, 584939179, 562222871, 564619, "SRX4505261", "SRS3625653", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.89313, 0.87302, 0.42444, 0.40784, 0.72096, 0.72393, 0.58673, 0.60423, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive System"], [59044, "SRR11585444", "SRX8152997", "SRS6515547", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC MUT 3", "GSM4490224", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Pax6b / ", "EEC MUT 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Pax6b / ", "GSM4490224", "GSM4490224: EEC MUT 3; Danio rerio; RNA Seq", "GSM4490224", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490224", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS14-B816_Y_TAAGGCGA_L006_R1_001.fastq.gz NGS14-B816_Y_TAAGGCGA_L006_R2_001.fastq.gz", "fastq fastq", 7305946100.0, 36168050.0, "GSM4490224 r1", "0:101 1:101", "A:2038766865;C:1613931139;G:1509805073;T:2128443712;N:14999311", 101, 101, null, null, 2038766865, 1613931139, 1509805073, 2128443712, 14999311, "SRX8152997", "SRS6515547", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.8749, 0.87565, 0.15943, 0.16056, 0.75365, 0.75402, 0.54284, 0.54869, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59045, "SRR11585443", "SRX8152996", "SRS6515546", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC MUT 2", "GSM4490223", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Pax6b / ", "EEC MUT 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Pax6b / ", "GSM4490223", "GSM4490223: EEC MUT 2; Danio rerio; RNA Seq", "GSM4490223", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490223", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS14-B812_7_CGTACTAG_L008_R2_001.fastq.gz NGS14-B812_7_CGTACTAG_L008_R1_001.fastq.gz", "fastq fastq", 11918410666.0, 59002033.0, "GSM4490223 r1", "0:101 1:101", "A:3329793292;C:2614866685;G:2397465569;T:3556331253;N:19953867", 101, 101, null, null, 3329793292, 2614866685, 2397465569, 3556331253, 19953867, "SRX8152996", "SRS6515546", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.86265, 0.86065, 0.18072, 0.18105, 0.7637, 0.76646, 0.48622, 0.58912, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59046, "SRR11585442", "SRX8152995", "SRS6515545", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC MUT 1", "GSM4490222", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Pax6b / ", "EEC MUT 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Pax6b / ", "GSM4490222", "GSM4490222: EEC MUT 1; Danio rerio; RNA Seq", "GSM4490222", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490222", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS14-B811_4_TAAGGCGA_L008_R1_001.fastq.gz NGS14-B811_4_TAAGGCGA_L008_R2_001.fastq.gz", "fastq fastq", 17357075836.0, 85926118.0, "GSM4490222 r1", "0:101 1:101", "A:4885184535;C:3776696530;G:3534374130;T:5131850822;N:28969819", 101, 101, null, null, 4885184535, 3776696530, 3534374130, 5131850822, 28969819, "SRX8152995", "SRS6515545", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.86595, 0.86596, 0.17082, 0.17065, 0.75469, 0.7569, 0.57569, 0.57998, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59047, "SRR11585441", "SRX8152994", "SRS6515544", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC WT 4", "GSM4490221", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "EEC WT 4", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "GSM4490221", "GSM4490221: EEC WT 4; Danio rerio; RNA Seq", "GSM4490221", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490221", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS14-B103_GutcDNA_GTGAAA_L001_R2_001.fastq.gz NGS14-B103_GutcDNA_GTGAAA_L001_R1_001.fastq.gz", "fastq fastq", 8611929024.0, 42633312.0, "GSM4490221 r1", "0:101 1:101", "A:2475490797;C:1609639919;G:1667747515;T:2814782248;N:44268545", 101, 101, null, null, 2475490797, 1609639919, 1667747515, 2814782248, 44268545, "SRX8152994", "SRS6515544", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.88123, 0.80064, 0.22747, 0.21643, 0.77195, 0.80781, 0.49886, 0.49179, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59048, "SRR11585440", "SRX8152993", "SRS6515543", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC WT 3", "GSM4490220", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "EEC WT 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "GSM4490220", "GSM4490220: EEC WT 3; Danio rerio; RNA Seq", "GSM4490220", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490220", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS14-B709_K_GGACTCCT_L005_R1_001.fastq.gz NGS14-B709_K_GGACTCCT_L005_R2_001.fastq.gz", "fastq fastq", 10354295578.0, 51258889.0, "GSM4490220 r1", "0:101 1:101", "A:2967030863;C:2195339515;G:2034968623;T:3128829625;N:28126952", 101, 101, null, null, 2967030863, 2195339515, 2034968623, 3128829625, 28126952, "SRX8152993", "SRS6515543", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.87011, 0.86185, 0.17853, 0.17636, 0.76435, 0.76609, 0.52736, 0.51806, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59049, "SRR11585439", "SRX8152992", "SRS6515542", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC WT 2", "GSM4490219", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "EEC WT 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "GSM4490219", "GSM4490219: EEC WT 2; Danio rerio; RNA Seq", "GSM4490219", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS14-B708_D_AGGCAGAA_L005_R1_001.fastq.gz NGS14-B708_D_AGGCAGAA_L005_R2_001.fastq.gz", "fastq fastq", 12045022246.0, 59628823.0, "GSM4490219 r1", "0:101 1:101", "A:3416690974;C:2604045484;G:2417147877;T:3574238685;N:32899226", 101, 101, null, null, 3416690974, 2604045484, 2417147877, 3574238685, 32899226, "SRX8152992", "SRS6515542", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.86842, 0.86282, 0.21951, 0.2191, 0.75532, 0.75879, 0.53544, 0.53713, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59050, "SRR11585438", "SRX8152991", "SRS6515541", "SRP257811", "PRJNA627266", "Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks", "GSE149081", "Transcriptome Analysis", "Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.", null, "pubmed:32867764;pubmed:35286299", null, "EEC WT 1", "GSM4490218", null, "source name:Enteroendocrine cells EECs|strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "EEC WT 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Enteroendocrine cells EECs", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Enteroendocrine cells|age:4 dpf|genotype:Wild type", "GSM4490218", "GSM4490218: EEC WT 1; Danio rerio; RNA Seq", "GSM4490218", null, "1", "Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the \u201cyield mode\u201d and the second in \u201cthe purity mode\u201d  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.", "GEO Accession:GSM4490218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP257811", null, null, "NGS15-D205_WT-4dpf_TAAGGCGA_L008_R2_001.fastq.gz NGS15-D205_WT-4dpf_TAAGGCGA_L008_R1_001.fastq.gz", "fastq fastq", 20091433484.0, 99462542.0, "GSM4490218 r1", "0:101 1:101", "A:5656340585;C:4375126690;G:4104085278;T:5941433597;N:14447334", 101, 101, null, null, 5656340585, 4375126690, 4104085278, 5941433597, 14447334, "SRX8152991", "SRS6515541", "SRA1067841", "GEO", "GIGA, University of Li\u00e8ge", 2, 0.86594, 0.86466, 0.15632, 0.15772, 0.76081, 0.76453, 0.53085, 0.53533, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2020-04-21", "Larval", "Larval", "Gut", "Digestive System"], [59220, "SRR11777254", "SRX8330121", "SRS6649608", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "Wide type in germ free condition rep2 [WT GF 2]", "GSM4547721", null, "source name:Wide type in germ free condition|strain background:AB|age:7 dpf type|treatment:germ free condition|tissue:larvae intestine", "Wide type in germ free condition rep2 [WT GF 2]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "Wide type in germ free condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf type|treatment:germ free condition|tissue:larvae intestine", "GSM4547721", "GSM4547721: Wide type in germ free condition rep2 [WT GF 2]; Danio rerio; RNA Seq", "GSM4547721", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547721", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "WT-GF-2_1.fastq.gz WT-GF-2_2.fastq.gz", "fastq fastq", 8496479358.0, 42061779.0, "GSM4547721 r1", "0:101 1:101", "A:2120538452;C:2126725496;G:2119304285;T:2129825105;N:86020", 101, 101, null, null, 2120538452, 2126725496, 2119304285, 2129825105, 86020, "SRX8330121", "SRS6649608", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.74356, 0.70337, 0.1439, 0.13679, 0.81049, 0.81677, 0.65725, 0.6459, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59221, "SRR11777253", "SRX8330120", "SRS6649607", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "Wide type in germ free condition rep1 [WT GF 1]", "GSM4547720", null, "source name:Wide type in germ free condition|strain background:AB|age:7 dpf type|treatment:germ free condition|tissue:larvae intestine", "Wide type in germ free condition rep1 [WT GF 1]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "Wide type in germ free condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf type|treatment:germ free condition|tissue:larvae intestine", "GSM4547720", "GSM4547720: Wide type in germ free condition rep1 [WT GF 1]; Danio rerio; RNA Seq", "GSM4547720", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "WT-GF-1_2.fastq.gz WT-GF-1_1.fastq.gz", "fastq fastq", 9086890614.0, 44984607.0, "GSM4547720 r1", "0:101 1:101", "A:2135115614;C:2392277049;G:2384587561;T:2174816084;N:94306", 101, 101, null, null, 2135115614, 2392277049, 2384587561, 2174816084, 94306, "SRX8330120", "SRS6649607", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.63452, 0.59771, 0.13257, 0.12635, 0.82962, 0.83867, 0.68321, 0.62132, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59222, "SRR11777252", "SRX8330119", "SRS6649606", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "Wide type in conventionally raised condition rep2 [WT CV 2]", "GSM4547719", null, "source name:Wide type in conventionally raised condition|strain background:AB|age:7 dpf type|treatment:conventionally raised condition|tissue:larvae intestine", "Wide type in conventionally raised condition rep2 [WT CV 2]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "Wide type in conventionally raised condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf type|treatment:conventionally raised condition|tissue:larvae intestine", "GSM4547719", "GSM4547719: Wide type in conventionally raised condition rep2 [WT CV 2]; Danio rerio; RNA Seq", "GSM4547719", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547719", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "WT-CV-2_1.fastq.gz WT-CV-2_2.fastq.gz", "fastq fastq", 8458913418.0, 41875809.0, "GSM4547719 r1", "0:101 1:101", "A:2076906648;C:2150093093;G:2142972201;T:2088851553;N:89923", 101, 101, null, null, 2076906648, 2150093093, 2142972201, 2088851553, 89923, "SRX8330119", "SRS6649606", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.70042, 0.63598, 0.13488, 0.12346, 0.82731, 0.83402, 0.70617, 0.63904, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59223, "SRR11777251", "SRX8330118", "SRS6649605", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "Wide type in conventionally raised condition rep1 [WT CV 1]", "GSM4547718", null, "source name:Wide type in conventionally raised condition|strain background:AB|age:7 dpf type|treatment:conventionally raised condition|tissue:larvae intestine", "Wide type in conventionally raised condition rep1 [WT CV 1]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "Wide type in conventionally raised condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf type|treatment:conventionally raised condition|tissue:larvae intestine", "GSM4547718", "GSM4547718: Wide type in conventionally raised condition rep1 [WT CV 1]; Danio rerio; RNA Seq", "GSM4547718", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547718", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "WT-CV-1_1.fastq.gz WT-CV-1_2.fastq.gz", "fastq fastq", 9288189270.0, 45981135.0, "GSM4547718 r1", "0:101 1:101", "A:2200780853;C:2427573007;G:2411847005;T:2247892664;N:95741", 101, 101, null, null, 2200780853, 2427573007, 2411847005, 2247892664, 95741, "SRX8330118", "SRS6649605", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.64725, 0.61001, 0.13549, 0.12962, 0.82917, 0.83782, 0.69442, 0.64636, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59224, "SRR11777250", "SRX8330117", "SRS6649604", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "tp53 mutant in germ free condition rep2 [P53 GF 2]", "GSM4547717", null, "source name:tp53 mutant in germ free condition|strain background:AB|age:7 dpf mutant|treatment:germ free condition|tissue:larvae intestine", "tp53 mutant in germ free condition rep2 [P53 GF 2]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "tp53 mutant in germ free condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf mutant|treatment:germ free condition|tissue:larvae intestine", "GSM4547717", "GSM4547717: tp53 mutant in germ free condition rep2 [P53 GF 2]; Danio rerio; RNA Seq", "GSM4547717", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547717", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "P53-GF-2_1.fastq.gz P53-GF-2_2.fastq.gz", "fastq fastq", 8788177660.0, 43505830.0, "GSM4547717 r1", "0:101 1:101", "A:2147869265;C:2240381993;G:2230578514;T:2169256177;N:91711", 101, 101, null, null, 2147869265, 2240381993, 2230578514, 2169256177, 91711, "SRX8330117", "SRS6649604", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.73539, 0.70687, 0.15857, 0.15095, 0.81128, 0.81809, 0.63358, 0.65063, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59225, "SRR11777249", "SRX8330116", "SRS6649603", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "tp53 mutant in germ free condition rep1 [P53 GF 1]", "GSM4547716", null, "source name:tp53 mutant in germ free condition|strain background:AB|age:7 dpf mutant|treatment:germ free condition|tissue:larvae intestine", "tp53 mutant in germ free condition rep1 [P53 GF 1]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "tp53 mutant in germ free condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf mutant|treatment:germ free condition|tissue:larvae intestine", "GSM4547716", "GSM4547716: tp53 mutant in germ free condition rep1 [P53 GF 1]; Danio rerio; RNA Seq", "GSM4547716", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547716", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "P53-GF-1_2.fastq.gz P53-GF-1_1.fastq.gz", "fastq fastq", 9001539756.0, 44562078.0, "GSM4547716 r1", "0:101 1:101", "A:2238688782;C:2250397957;G:2239868446;T:2272493135;N:91436", 101, 101, null, null, 2238688782, 2250397957, 2239868446, 2272493135, 91436, "SRX8330116", "SRS6649603", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.74988, 0.71692, 0.16488, 0.15853, 0.79673, 0.80531, 0.64241, 0.64263, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59226, "SRR11777248", "SRX8330115", "SRS6649602", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "tp53 mutant in conventionally raised condition rep2 [P53 CV 2]", "GSM4547715", null, "source name:tp53 mutant in conventionally raised condition|strain background:AB|age:7 dpf mutant|treatment:conventionally raised condition|tissue:larvae intestine", "tp53 mutant in conventionally raised condition rep2 [P53 CV 2]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "tp53 mutant in conventionally raised condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf mutant|treatment:conventionally raised condition|tissue:larvae intestine", "GSM4547715", "GSM4547715: tp53 mutant in conventionally raised condition rep2 [P53 CV 2]; Danio rerio; RNA Seq", "GSM4547715", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547715", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "P53-CV-2_2.fastq.gz P53-CV-2_1.fastq.gz", "fastq fastq", 11447791268.0, 56672234.0, "GSM4547715 r1", "0:101 1:101", "A:2899821061;C:2807713057;G:2785490114;T:2954649447;N:117589", 101, 101, null, null, 2899821061, 2807713057, 2785490114, 2954649447, 117589, "SRX8330115", "SRS6649602", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.7899, 0.76325, 0.16845, 0.16179, 0.79338, 0.80119, 0.6617, 0.65495, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59227, "SRR11777247", "SRX8330114", "SRS6649601", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "tp53 mutant in conventionally raised condition rep1 [P53 CV 1]", "GSM4547714", null, "source name:tp53 mutant in conventionally raised condition|strain background:AB|age:7 dpf mutant|treatment:conventionally raised condition|tissue:larvae intestine", "tp53 mutant in conventionally raised condition rep1 [P53 CV 1]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "tp53 mutant in conventionally raised condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf mutant|treatment:conventionally raised condition|tissue:larvae intestine", "GSM4547714", "GSM4547714: tp53 mutant in conventionally raised condition rep1 [P53 CV 1]; Danio rerio; RNA Seq", "GSM4547714", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547714", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "P53-CV-1_1.fastq.gz P53-CV-1_2.fastq.gz", "fastq fastq", 9648437080.0, 47764540.0, "GSM4547714 r1", "0:101 1:101", "A:2366724359;C:2441716821;G:2430001317;T:2409892181;N:102402", 101, 101, null, null, 2366724359, 2441716821, 2430001317, 2409892181, 102402, "SRX8330114", "SRS6649601", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.70691, 0.67838, 0.15555, 0.14908, 0.80438, 0.81201, 0.62653, 0.64318, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive System"], [59228, "SRR12974176", "SRX9426454", "SRS7641325", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM10", "GSM4878631", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3", "SNJM10", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878631", "GSM4878631: SNJM10; Danio rerio; RNA Seq", "GSM4878631", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878631", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM10 0 G S10 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM10 0 G S10 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM10 0 G S10 L001 R2 001.fastq.gz", "JUCH10_SNJM10_0_G_S10_L001_I1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L001_R1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L001_R2_001.fastq.gz", "fastq fastq fastq", 9612906312.0, 103364584.0, "GSM4878631 r1", "0:8 1:29 2:56", "A:2566209216;C:2292038760;G:2265576943;T:2488871493;N:209900", 8, 29, 56, null, 2566209216, 2292038760, 2265576943, 2488871493, 209900, "SRX9426454", "SRS7641325", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.962, null, 0.0608, null, 0.8734, null, 0.67588, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59229, "SRR12974177", "SRX9426454", "SRS7641325", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM10", "GSM4878631", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3", "SNJM10", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878631", "GSM4878631: SNJM10; Danio rerio; RNA Seq", "GSM4878631", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878631", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM10 0 G S10 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM10 0 G S10 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM10 0 G S10 L002 R2 001.fastq.gz", "JUCH10_SNJM10_0_G_S10_L002_I1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L002_R1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L002_R2_001.fastq.gz", "fastq fastq fastq", 9545302752.0, 102637664.0, "GSM4878631 r2", "0:8 1:29 2:56", "A:2548745985;C:2274433644;G:2248703958;T:2472613589;N:805576", 8, 29, 56, null, 2548745985, 2274433644, 2248703958, 2472613589, 805576, "SRX9426454", "SRS7641325", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9615, null, 0.06194, null, 0.87247, null, 0.74516, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59230, "SRR12974174", "SRX9426453", "SRS7641324", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM09", "GSM4878630", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3", "SNJM09", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878630", "GSM4878630: SNJM09; Danio rerio; RNA Seq", "GSM4878630", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878630", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM9 0 G S9 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM9 0 G S9 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM9 0 G S9 L001 R2 001.fastq.gz", "JUCH10_SNJM9_0_G_S9_L001_I1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L001_R1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L001_R2_001.fastq.gz", "fastq fastq fastq", 9550986633.0, 102698781.0, "GSM4878630 r1", "0:8 1:29 2:56", "A:2545306811;C:2315371452;G:2200128862;T:2489970955;N:208553", 8, 29, 56, null, 2545306811, 2315371452, 2200128862, 2489970955, 208553, "SRX9426453", "SRS7641324", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96301, null, 0.05192, null, 0.88743, null, 0.70057, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59231, "SRR12974175", "SRX9426453", "SRS7641324", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM09", "GSM4878630", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3", "SNJM09", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878630", "GSM4878630: SNJM09; Danio rerio; RNA Seq", "GSM4878630", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878630", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM9 0 G S9 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM9 0 G S9 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM9 0 G S9 L002 R2 001.fastq.gz", "JUCH10_SNJM9_0_G_S9_L002_I1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L002_R1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L002_R2_001.fastq.gz", "fastq fastq fastq", 9486231849.0, 102002493.0, "GSM4878630 r2", "0:8 1:29 2:56", "A:2528707184;C:2298013878;G:2184508040;T:2474200996;N:801751", 8, 29, 56, null, 2528707184, 2298013878, 2184508040, 2474200996, 801751, "SRX9426453", "SRS7641324", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96301, null, 0.05148, null, 0.8846, null, 0.72241, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59232, "SRR12974172", "SRX9426452", "SRS7641323", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM08", "GSM4878629", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3", "SNJM08", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3", "GSM4878629", "GSM4878629: SNJM08; Danio rerio; RNA Seq", "GSM4878629", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878629", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM8 0 G S8 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM8 0 G S8 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM8 0 G S8 L001 R2 001.fastq.gz", "JUCH10_SNJM8_0_G_S8_L001_I1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L001_R1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L001_R2_001.fastq.gz", "fastq fastq fastq", 10406956308.0, 111902756.0, "GSM4878629 r1", "0:8 1:29 2:56", "A:2870124713;C:2509365613;G:2345749207;T:2681489991;N:226784", 8, 29, 56, null, 2870124713, 2509365613, 2345749207, 2681489991, 226784, "SRX9426452", "SRS7641323", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96215, null, 0.03963, null, 0.90057, null, 0.84217, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59233, "SRR12974173", "SRX9426452", "SRS7641323", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM08", "GSM4878629", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3", "SNJM08", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3", "GSM4878629", "GSM4878629: SNJM08; Danio rerio; RNA Seq", "GSM4878629", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878629", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM8 0 G S8 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM8 0 G S8 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM8 0 G S8 L002 R2 001.fastq.gz", "JUCH10_SNJM8_0_G_S8_L002_I1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L002_R1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L002_R2_001.fastq.gz", "fastq fastq fastq", 10347171444.0, 111259908.0, "GSM4878629 r2", "0:8 1:29 2:56", "A:2855106653;C:2493008676;G:2331251314;T:2666929711;N:875090", 8, 29, 56, null, 2855106653, 2493008676, 2331251314, 2666929711, 875090, "SRX9426452", "SRS7641323", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96136, null, 0.03986, null, 0.90021, null, 0.83819, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59234, "SRR12974170", "SRX9426451", "SRS7641322", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM07", "GSM4878628", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3", "SNJM07", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3", "GSM4878628", "GSM4878628: SNJM07; Danio rerio; RNA Seq", "GSM4878628", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878628", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM7 0 G S7 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM7 0 G S7 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM7 0 G S7 L001 R2 001.fastq.gz", "JUCH10_SNJM7_0_G_S7_L001_I1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L001_R1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L001_R2_001.fastq.gz", "fastq fastq fastq", 9123196584.0, 98098888.0, "GSM4878628 r1", "0:8 1:29 2:56", "A:2569669307;C:2214757071;G:1969962475;T:2368609155;N:198576", 8, 29, 56, null, 2569669307, 2214757071, 1969962475, 2368609155, 198576, "SRX9426451", "SRS7641322", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96088, null, 0.05866, null, 0.88708, null, 0.85062, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59235, "SRR12974171", "SRX9426451", "SRS7641322", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM07", "GSM4878628", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3", "SNJM07", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3", "GSM4878628", "GSM4878628: SNJM07; Danio rerio; RNA Seq", "GSM4878628", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878628", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM7 0 G S7 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM7 0 G S7 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM7 0 G S7 L002 R2 001.fastq.gz", "JUCH10_SNJM7_0_G_S7_L002_I1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L002_R1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L002_R2_001.fastq.gz", "fastq fastq fastq", 9055633293.0, 97372401.0, "GSM4878628 r2", "0:8 1:29 2:56", "A:2551775269;C:2196748202;G:1954504090;T:2351840767;N:764965", 8, 29, 56, null, 2551775269, 2196748202, 1954504090, 2351840767, 764965, "SRX9426451", "SRS7641322", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96058, null, 0.05844, null, 0.88939, null, 0.85033, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59236, "SRR12974168", "SRX9426450", "SRS7641321", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM06", "GSM4878627", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3", "SNJM06", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3", "GSM4878627", "GSM4878627: SNJM06; Danio rerio; RNA Seq", "GSM4878627", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878627", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM6 0 G S6 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM6 0 G S6 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM6 0 G S6 L001 R2 001.fastq.gz", "JUCH10_SNJM6_0_G_S6_L001_I1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L001_R1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L001_R2_001.fastq.gz", "fastq fastq fastq", 8956677015.0, 96308355.0, "GSM4878627 r1", "0:8 1:29 2:56", "A:2473315824;C:2129478747;G:2022150123;T:2331535818;N:196503", 8, 29, 56, null, 2473315824, 2129478747, 2022150123, 2331535818, 196503, "SRX9426450", "SRS7641321", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96363, null, 0.04651, null, 0.89988, null, 0.84067, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59237, "SRR12974169", "SRX9426450", "SRS7641321", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM06", "GSM4878627", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3", "SNJM06", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3", "GSM4878627", "GSM4878627: SNJM06; Danio rerio; RNA Seq", "GSM4878627", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878627", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM6 0 G S6 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM6 0 G S6 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM6 0 G S6 L002 R2 001.fastq.gz", "JUCH10_SNJM6_0_G_S6_L002_I1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L002_R1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L002_R2_001.fastq.gz", "fastq fastq fastq", 8891805795.0, 95610815.0, "GSM4878627 r2", "0:8 1:29 2:56", "A:2456331697;C:2112784685;G:2006505048;T:2315434557;N:749808", 8, 29, 56, null, 2456331697, 2112784685, 2006505048, 2315434557, 749808, "SRX9426450", "SRS7641321", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96343, null, 0.04559, null, 0.90165, null, 0.84056, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59238, "SRR12974166", "SRX9426449", "SRS7641320", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM05", "GSM4878626", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3", "SNJM05", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3", "GSM4878626", "GSM4878626: SNJM05; Danio rerio; RNA Seq", "GSM4878626", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878626", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM5 0 G S5 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM5 0 G S5 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM5 0 G S5 L001 R2 001.fastq.gz", "JUCH10_SNJM5_0_G_S5_L001_I1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L001_R1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L001_R2_001.fastq.gz", "fastq fastq fastq", 9064946499.0, 97472543.0, "GSM4878626 r1", "0:8 1:29 2:56", "A:2554844989;C:2175928954;G:1956415280;T:2377558346;N:198930", 8, 29, 56, null, 2554844989, 2175928954, 1956415280, 2377558346, 198930, "SRX9426449", "SRS7641320", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96742, null, 0.0357, null, 0.91737, null, 0.88943, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59239, "SRR12974167", "SRX9426449", "SRS7641320", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM05", "GSM4878626", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3", "SNJM05", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3", "GSM4878626", "GSM4878626: SNJM05; Danio rerio; RNA Seq", "GSM4878626", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878626", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM5 0 G S5 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM5 0 G S5 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM5 0 G S5 L002 R2 001.fastq.gz", "JUCH10_SNJM5_0_G_S5_L002_I1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L002_R1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L002_R2_001.fastq.gz", "fastq fastq fastq", 8995948497.0, 96730629.0, "GSM4878626 r2", "0:8 1:29 2:56", "A:2536668919;C:2157506999;G:1940651397;T:2360359924;N:761258", 8, 29, 56, null, 2536668919, 2157506999, 1940651397, 2360359924, 761258, "SRX9426449", "SRS7641320", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96676, null, 0.03558, null, 0.91666, null, 0.88967, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59240, "SRR12974164", "SRX9426448", "SRS7641318", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM04", "GSM4878625", null, "source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3", "SNJM04", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878625", "GSM4878625: SNJM04; Danio rerio; RNA Seq", "GSM4878625", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878625", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM4 0 G S4 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM4 0 G S4 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM4 0 G S4 L001 R2 001.fastq.gz", "JUCH10_SNJM4_0_G_S4_L001_I1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L001_R1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 9600834633.0, 103234781.0, "GSM4878625 r1", "0:8 1:29 2:56", "A:2687588051;C:2283954081;G:2107499458;T:2521583198;N:209845", 8, 29, 56, null, 2687588051, 2283954081, 2107499458, 2521583198, 209845, "SRX9426448", "SRS7641318", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95608, null, 0.06784, null, 0.8538, null, 0.81465, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59241, "SRR12974165", "SRX9426448", "SRS7641318", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM04", "GSM4878625", null, "source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3", "SNJM04", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878625", "GSM4878625: SNJM04; Danio rerio; RNA Seq", "GSM4878625", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878625", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM4 0 G S4 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM4 0 G S4 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM4 0 G S4 L002 R2 001.fastq.gz", "JUCH10_SNJM4_0_G_S4_L002_I1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L002_R1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 9548851539.0, 102675823.0, "GSM4878625 r2", "0:8 1:29 2:56", "A:2673944918;C:2269787019;G:2095420445;T:2508893277;N:805880", 8, 29, 56, null, 2673944918, 2269787019, 2095420445, 2508893277, 805880, "SRX9426448", "SRS7641318", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95602, null, 0.06682, null, 0.85433, null, 0.61345, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59242, "SRR12974162", "SRX9426447", "SRS7641319", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM03", "GSM4878624", null, "source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3", "SNJM03", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3", "GSM4878624", "GSM4878624: SNJM03; Danio rerio; RNA Seq", "GSM4878624", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878624", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM3 0 G S3 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM3 0 G S3 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM3 0 G S3 L001 R2 001.fastq.gz", "JUCH10_SNJM3_0_G_S3_L001_I1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L001_R1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 9157702932.0, 98469924.0, "GSM4878624 r1", "0:8 1:29 2:56", "A:2627894488;C:2152254884;G:2064675616;T:2312678653;N:199291", 8, 29, 56, null, 2627894488, 2152254884, 2064675616, 2312678653, 199291, "SRX9426447", "SRS7641319", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95169, null, 0.08321, null, 0.8802, null, 0.7957, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59243, "SRR12974163", "SRX9426447", "SRS7641319", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM03", "GSM4878624", null, "source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3", "SNJM03", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3", "GSM4878624", "GSM4878624: SNJM03; Danio rerio; RNA Seq", "GSM4878624", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878624", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM3 0 G S3 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM3 0 G S3 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM3 0 G S3 L002 R2 001.fastq.gz", "JUCH10_SNJM3_0_G_S3_L002_I1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L002_R1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 9084747687.0, 97685459.0, "GSM4878624 r2", "0:8 1:29 2:56", "A:2607939019;C:2133198115;G:2047005553;T:2295838531;N:766469", 8, 29, 56, null, 2607939019, 2133198115, 2047005553, 2295838531, 766469, "SRX9426447", "SRS7641319", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95159, null, 0.08346, null, 0.87799, null, 0.86901, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59244, "SRR12974160", "SRX9426446", "SRS7641317", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM02", "GSM4878623", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3", "SNJM02", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878623", "GSM4878623: SNJM02; Danio rerio; RNA Seq", "GSM4878623", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878623", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM2 0 G S2 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM2 0 G S2 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM2 0 G S2 L001 R2 001.fastq.gz", "JUCH10_SNJM2_0_G_S2_L001_I1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L001_R1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 9141163440.0, 98292080.0, "GSM4878623 r1", "0:8 1:29 2:56", "A:2568403174;C:2203993337;G:1949600715;T:2418964898;N:201316", 8, 29, 56, null, 2568403174, 2203993337, 1949600715, 2418964898, 201316, "SRX9426446", "SRS7641317", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96372, null, 0.04508, null, 0.89416, null, 0.89922, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59245, "SRR12974161", "SRX9426446", "SRS7641317", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM02", "GSM4878623", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3", "SNJM02", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3", "GSM4878623", "GSM4878623: SNJM02; Danio rerio; RNA Seq", "GSM4878623", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878623", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM2 0 G S2 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM2 0 G S2 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM2 0 G S2 L002 R2 001.fastq.gz", "JUCH10_SNJM2_0_G_S2_L002_I1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L002_R1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 9095463519.0, 97800683.0, "GSM4878623 r2", "0:8 1:29 2:56", "A:2556536997;C:2191496444;G:1938967545;T:2407692037;N:770496", 8, 29, 56, null, 2556536997, 2191496444, 1938967545, 2407692037, 770496, "SRX9426446", "SRS7641317", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96463, null, 0.044, null, 0.89286, null, 0.90213, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59246, "SRR12974158", "SRX9426445", "SRS7641316", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM01", "GSM4878622", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3", "SNJM01", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3", "GSM4878622", "GSM4878622: SNJM01; Danio rerio; RNA Seq", "GSM4878622", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878622", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM1 0 G S1 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM1 0 G S1 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM1 0 G S1 L001 R2 001.fastq.gz", "JUCH10_SNJM1_0_G_S1_L001_I1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L001_R1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 9359347578.0, 100638146.0, "GSM4878622 r1", "0:8 1:29 2:56", "A:2742192040;C:2208968705;G:2007446927;T:2400535057;N:204849", 8, 29, 56, null, 2742192040, 2208968705, 2007446927, 2400535057, 204849, "SRX9426445", "SRS7641316", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.97296, null, 0.04791, null, 0.91259, null, 0.93709, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59247, "SRR12974159", "SRX9426445", "SRS7641316", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM01", "GSM4878622", null, "source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3", "SNJM01", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3", "GSM4878622", "GSM4878622: SNJM01; Danio rerio; RNA Seq", "GSM4878622", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878622", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM1 0 G S1 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM1 0 G S1 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM1 0 G S1 L002 R2 001.fastq.gz", "JUCH10_SNJM1_0_G_S1_L002_I1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L002_R1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 9286776051.0, 99857807.0, "GSM4878622 r2", "0:8 1:29 2:56", "A:2721584053;C:2190402119;G:1990556025;T:2383450199;N:783655", 8, 29, 56, null, 2721584053, 2190402119, 1990556025, 2383450199, 783655, "SRX9426445", "SRS7641316", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9733, null, 0.04761, null, 0.91441, null, 0.93019, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "Larval", "Larval", "Gut", "Digestive System"], [59248, "SRR11785641", "SRX8337992", "SRS6656491", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "source name:Intestinal dissection|tissue:Intestine|status:DSS treated", "SNJC03", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|status:DSS treated", "GSM4551420", "GSM4551420: SNJC03; Danio rerio; RNA Seq", "GSM4551420", null, "1", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "GEO Accession:GSM4551420", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC03 S5 L001 I1 001.fastq.gz   read2PairFiles=SNJC03 S5 L001 R1 001.fastq.gz   read3PairFiles=SNJC03 S5 L001 R2 001.fastq.gz", "SNJC03_S5_L001_R2_001.fastq.gz SNJC03_S5_L001_R1_001.fastq.gz SNJC03_S5_L001_I1_001.fastq.gz", "fastq fastq fastq", 1187350424.0, 13341016.0, "GSM4551420 r1", "0:8 1:26 2:55", "A:333004523;C:277828258;G:286036018;T:290210763;N:270862", 8, 26, 55, null, 333004523, 277828258, 286036018, 290210763, 270862, "SRX8337992", "SRS6656491", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.94136, null, 0.10077, null, 0.85512, null, 0.75118, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-05-13", "Larval", "Larval", "Gut", "Digestive System"], [59249, "SRR11785642", "SRX8337992", "SRS6656491", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "source name:Intestinal dissection|tissue:Intestine|status:DSS treated", "SNJC03", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|status:DSS treated", "GSM4551420", "GSM4551420: SNJC03; Danio rerio; RNA Seq", "GSM4551420", null, "1", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "GEO Accession:GSM4551420", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC03 S5 L002 I1 001.fastq.gz   read2PairFiles=SNJC03 S5 L002 R1 001.fastq.gz   read3PairFiles=SNJC03 S5 L002 R2 001.fastq.gz", "SNJC03_S5_L002_R2_001.fastq.gz SNJC03_S5_L002_R1_001.fastq.gz SNJC03_S5_L002_I1_001.fastq.gz", "fastq fastq fastq", 1308643451.0, 14703859.0, "GSM4551420 r2", "0:8 1:26 2:55", "A:366398712;C:306757422;G:316095972;T:319052449;N:338896", 8, 26, 55, null, 366398712, 306757422, 316095972, 319052449, 338896, "SRX8337992", "SRS6656491", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9424, null, 0.09777, null, 0.85188, null, 0.75485, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-05-13", "Larval", "Larval", "Gut", "Digestive System"], [59250, "SRR11785643", "SRX8337992", "SRS6656491", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "source name:Intestinal dissection|tissue:Intestine|status:DSS treated", "SNJC03", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|status:DSS treated", "GSM4551420", "GSM4551420: SNJC03; Danio rerio; RNA Seq", "GSM4551420", null, "1", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. 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Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "source name:Intestinal dissection|tissue:Intestine|status:DSS treated", "SNJC03", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|status:DSS treated", "GSM4551420", "GSM4551420: SNJC03; Danio rerio; RNA Seq", "GSM4551420", null, "1", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. 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Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJC02", "GSM4551419", null, "source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl", "SNJC02", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|status:untreated ctrl", "GSM4551419", "GSM4551419: SNJC02; Danio rerio; RNA Seq", "GSM4551419", null, "1", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. 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Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJC02", "GSM4551419", null, "source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl", "SNJC02", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|status:untreated ctrl", "GSM4551419", "GSM4551419: SNJC02; Danio rerio; RNA Seq", "GSM4551419", null, "1", "post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. 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