{"database": "metadata", "table": "run_metadata", "rows": [[71632, "SRR21855290", "SRX17843605", "SRS15365430", "SRP401856", "PRJNA889065", "A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish", "GSE215189", "Transcriptome Analysis", "T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.", null, "pubmed:37155881", null, "Infected  scRNAseq", "GSM6625507", null, "tissue:Descaled cells|cell type:Descaled cells|treatment:infected", "Infected  scRNAseq", "Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files", "Descaled cells", null, "Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter\u2019s instructions Chromium Single Cell Gene Expression Solution 3\u2019 v2  10x Genomics.", null, "cell type:Descaled cells|treatment:infected", "GSM6625507", "GSM6625507: Infected  scRNAseq; Danio rerio; RNA Seq", "GSM6625507 r1", "GSM6625507", "1", "Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP401856", null, "loader:fastq load.py", "Infected_S2_L001_R1_001.fastq.gz Infected_S2_L001_R2_001.fastq.gz", "fastq fastq", 27971148231.0, 239069643.0, "GSM6625507 r1", "0:28 1:89", "A:8061885724;C:6040148313;G:6562354866;T:7306186742;N:572586", 28, 89, null, null, 8061885724, 6040148313, 6562354866, 7306186742, 572586, "SRX17843605", "SRS15365430", "SRA1517576", "Ting Wang, Genetics, Washington University St Louis", "Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health", 2, 0.00829, 0.90109, 0.0031, 0.16974, 0.98742, 0.79249, 0.29098, 0.56795, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-10", "Adult", "Adult", "Scale", "Surface Structure"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["71632"], "units": {}, "query_ms": 11.445627998909913}