{"database": "metadata", "table": "run_metadata", "rows": [[76639, "SRR25247897", "SRX20994111", "SRS18268517", "SRP448831", "PRJNA994052", "Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model", "GSE237139", "Transcriptome Analysis", "The thymus is the site of T lymphocyte development and T cell education to recognize foreign  but not self  antigens. B cells also reside and develop in the thymus  although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation  thymic cells decline. However  thymic B cells decrease far less than T cells  such that B cells comprise 1% of neonatal thymocytes  but up to 10% in maturity in humans. All jawed vertebrates possess a thymus  and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here  we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific  fluorophore labeled transgenic lines  quantifying changes in thymic lymphocytes pre  vs. post involution. Our results prove that  as in humans  zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines  identifying distinct populations of immature T and B cells. Collectively  this is the first comprehensive analysis of zebrafish thymic involution  demonstrating its similarity to human involution  and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically  four different double transgenic zebrafish lines were utilized  each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79aGFP  Population M1  Sample 55", "GSM7595976", null, "source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Marrow  lckmCherry cd79aGFP  Population M1  Sample 55", "Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing  the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread  v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing  library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample", "Marrow", null, "Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD following manufacturer's protocols.", "For procedures  zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.", "tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595976", "GSM7595976: Marrow  lckmCherry cd79aGFP  Population M1  Sample 55; Danio rerio; RNA Seq", "GSM7595976 r1", "GSM7595976", "1", "Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "55_S67_R1_001.fastq.gz 55_S67_R2_001.fastq.gz", "fastq fastq", 9888413482.0, 32743091.0, "GSM7595976 r1", "0:151 1:151", "A:2884186543;C:1849928947;G:2064604866;T:3089653973;N:39153", 151, 151, null, null, 2884186543, 1849928947, 2064604866, 3089653973, 39153, "SRX20994111", "SRS18268517", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.74087, 0.57449, 0.10781, 0.10777, 0.88937, 0.93768, 0.69241, 0.41557, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"]], "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": ["76639"], "units": {}, "query_ms": 10.092462005559355}