run_metadata: 71634

This data as json

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
71634	SRR21855292	SRX17843604	SRS15365429	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.		pubmed:37155881		Control scRNAseq	GSM6625506		tissue:Descaled cells\|cell type:Descaled cells\|treatment:control	Control 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		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 3’ v2 10x Genomics.		cell type:Descaled cells\|treatment:control	GSM6625506	GSM6625506: Control scRNAseq; Danio rerio; RNA Seq	GSM6625506 r1	GSM6625506	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP401856		loader:fastq load.py	Control_S1_L001_R1_001.fastq.gz Control_S1_L001_R2_001.fastq.gz	fastq fastq	22227506496.0	189978688.0	GSM6625506 r1	0:28 1:89	A:6692049340;C:4739918301;G:5329051962;T:5466033150;N:453743	28	89			6692049340	4739918301	5329051962	5466033150	453743	SRX17843604	SRS15365429	SRA1517576	Ting Wang, Genetics, Washington University St Louis	Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health	2	0.01277	0.88905	0.00634	0.17657	0.98879	0.78119	0.33278	0.56433	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x		United States	2022-10-10	Adult	Adult	Scale	Surface Structure