{"database": "metadata", "table": "run_metadata", "rows": [[30662, "SRR28125659", "SRX23770350", "SRS20595835", "SRP492124", "PRJNA1081449", "Thymic mimetic cells in zebrafish", "GSE259418", "Transcriptome Analysis", "We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells  a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically  we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067  GSM5732070  GSM5732077   GSM5732078  GSM5732079  GSM5732080  GSM5732081  GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition  we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII  whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching  filtering  and cell sorting. The live  non autofluorescent  GFP negative  mCherry negative cells a population depleted of T and B cells  thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult  Thymus  3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult  Thymus  4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult  Thymus  1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult  Thymus  2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile  Thymus  1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile  Thymus  2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile  Thymus  3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile  Thymus  4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5", null, null, null, "adult thy untreated", "GSM8115869", null, "tissue:13 wpf wpf loc name:missing|collection date:missing", "adult thy untreated", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms", "13 wpf", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "tissue:13 wpf", "GSM8115869", "GSM8115869: adult thy untreated; Danio rerio; RNA Seq", "GSM8115869 r1", "GSM8115869", "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP492124", null, "loader:fastq load.py", "adult_thy_untreated_S5_L001_R2_001.fastq.gz adult_thy_untreated_S5_L001_R1_001.fastq.gz adult_thy_untreated_S5_L001_I1_001.fastq.gz", "fastq fastq fastq", 61867658967.0, 487146921.0, "GSM8115869 r1", "0:8 1:28 2:91", "A:12933400034;C:9373762639;G:10188374364;T:11834295354;N:537420", 8, 28, 91, null, 12933400034, 9373762639, 10188374364, 11834295354, 537420, "SRX23770350", "SRS20595835", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.90847, null, 0.19603, null, 0.76895, null, 0.56494, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-27", "Multi-stage", "Multi-stage", "Undetermined", "Undetermined"]], "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": ["30662"], "units": {}, "query_ms": 9.78369900258258}