{"database": "metadata", "table": "run_metadata", "rows": [[57171, "SRR11243180", "SRX7854786", "SRS6264269", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "4.5 dpf CHT cells", "GSM4384818", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "4.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384818", "GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384818", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353H-CHT-4dpf_3_2_R1.fq.gz 171353H-CHT-4dpf_3_2_R2.fq.gz", "fastq fastq", 30131096700.0, 100436989.0, "GSM4384818 r1", "0:150 1:150", "A:6727746568;C:5761021689;G:10040248562;T:7601697440;N:382441", 150, 150, null, null, 6727746568, 5761021689, 10040248562, 7601697440, 382441, "SRX7854786", "SRS6264269", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.9175, 0.0, 0.06023, 1.0, 0.84208, null, 0.51614, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic 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": ["57171"], "units": {}, "query_ms": 8.989485002530273}