{"database": "metadata", "table": "run_metadata", "rows": [[66718, "SRR16490737", "SRX12693840", "SRS10644723", "SRP342163", "PRJNA772751", "Single cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species", "GSE186158", "Other", "We utilized single cell RNA sequencing scRNA seq to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species. Overall design: High dimensional single cell RNA sequencing 10X Genomics was used to profile the transcriptomes of total immune cells isolated from seven organism  spleens.", null, "pubmed:36871615", null, "Fish", "GSM5639492", null, "tissue:Fish splenocytes|cell type:Splenocytes", "Fish", "The 10x Genomics Cell Ranger 3.0.1 version pipeline was used to demultiplex raw files into FASTQ files  extract barcodes and UMI  filter  and map reads to the corresponding reference genome  and generate a matrix containing UMI counts. A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings. Genome build: Fish:GRCz11  Frog:Xenopus laevis v2  Mouse:GRCm38  Rat:Rnor 6.0  Pig:Sscrofa11  Monkey:Mmul 8  Human:GRCh38 Supplementary files format and content: Supplementary files format and content: filtered feature bc matrix.tar contains counts matrix stored in the Market Exchange Format for sparse matrices.", "Fish splenocytes", "Splenocytes were sorted from the spleens of  seven vertebrate species", "Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer 2% FBS in PBS  then passed through a 70 \u03bcm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK Ammonium Chloride Potassium Lysing Buffer to remove the red blood cells. post washing with 10 ml cold FACS buffer  the remaining cells were stained with 7AAD Part 76332; Lot B226294 Biolegend for 30 min at 4 \u00b0C  then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter BD Biosciences. Sorted 7AAD  cells with a viability higher than 90% were used for 10X genomics scRNA seq. Finally  libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit 300 cycles. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "cell type:Splenocytes", "GSM5639492", "GSM5639492: Fish; Danio rerio; RNA Seq", "GSM5639492 r1", "GSM5639492", "1", "Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer 2% FBS in PBS  then passed through a 70 \u03bcm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK Ammonium Chloride Potassium Lysing Buffer to remove the red blood cells. post washing with 10 ml cold FACS buffer  the remaining cells were stained with 7AAD Part 76332; Lot B226294 Biolegend for 30 min at 4 \u00b0C  then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter BD Biosciences. Sorted 7AAD  cells with a viability higher than 90% were used for 10X genomics scRNA seq. Finally  libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit 300 cycles. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342163", null, null, "fish5_S1_L002_R1_001.fastq.gz fish5_S1_L002_R2_001.fastq.gz", "fastq fastq", 128052138306.0, 424013703.0, "GSM5639492 r1", "0:151 1:151", "A:31857061588;C:30793041207;G:30850699878;T:34545754656;N:5580977", 151, 151, null, null, 31857061588, 30793041207, 30850699878, 34545754656, 5580977, "SRX12693840", "SRS10644723", "SRA1377133", "xian jiaotong university", "xian jiaotong university", 2, 0.06618, 0.94142, 0.01504, 0.09555, 0.96631, 0.81266, 0.69482, 0.58057, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Undetermined", "Undetermined", "Multi-tissue", "Multi-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": ["66718"], "units": {}, "query_ms": 10.087592999752815}