run_metadata: 33007
This data as json
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| 33007 | SRR29551178 | SRX25058395 | SRS21755348 | SRP516116 | PRJNA1128236 | The axillary lymphoid organ an external experimentally accessible immune organ in the zebrafish | GSE270797 | Other | Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals but the deep internal locations of these organs makes it challenging to study dynamic cellular mechanisms of immune cell interaction with pathogens or other host tissues such as the vasculature in living animals. Here we describe a previously uncharacterized external immune organ located near the base of the zebrafish pectoral fin the pectoral axillary lobe PAL with a variety of features that make it ideally suited for studying immune cell dynamics in vivo. This small transparent organ consists of an outer cortex teeming with immune cells and an inner medulla with a mesh like network of fibroblastic reticular cells along which immune cells migrate and a network of lymphatic vessels draining to a large adjacent lymph sac. Noninvasive high resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals and the PAL is readily accessible to external treatment with antigens or pathogens. This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues including blood and lymphatic vessels. Overall design: Single cell expression profiling by high throughput sequencing | pubmed:39091802 | Pectoral axillary lobe scRNA | GSM8352182 | source name:Pectoral axillary lobe|tissue:Pectoral axillary lobe|geo loc name:missing|collection date:missing | Pectoral axillary lobe scRNA | cellranger count v7.0.0 Assembly: zv11 Supplementary files format and content: TSV value and matrix files | Pectoral axillary lobe | Cell suspension prepared from 4 pectoral axillary lobes 2 from males 2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations | tissue:Pectoral axillary lobe | GSM8352182 | GSM8352182: Pectoral axillary lobe scRNA; Danio rerio; RNA Seq | GSM8352182 r1 | GSM8352182 | 1 | Cell suspension prepared from 4 pectoral axillary lobes 2 from males 2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP516116 | LCK1_S3_L001_R1_001.fastq.gz LCK1_S3_L001_R2_001.fastq.gz LCK1_S3_L002_R1_001.fastq.gz LCK1_S3_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 21583802440.0 | 182913580.0 | GSM8352182 r1 | 0:28 1:90 | A:6079984051;C:4913875575;G:5182513698;T:5406578531;N:850585 | 28 | 90 | 6079984051 | 4913875575 | 5182513698 | 5406578531 | 850585 | SRX25058395 | SRS21755348 | SRA1909244 | BG 10 RM 8S261, NICHD, NIH | BG 10 RM 8S261, NICHD, NIH | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-06-25 | Adult | Adult | Undetermined | Undetermined |