{"database": "metadata", "table": "run_metadata", "rows": [[49407, "SRR7904991", "SRX4741349", "SRS3822681", "SRP162658", "PRJNA493234", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]", "GSE120503", "Other", "To investigate the peculiarity of CHT HSPCs  as well as the interaction of CHT niche and HSPCs at higher resolution  we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "52 hpf CHT cells", "GSM3402061", null, "tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "52 hpf 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 samples  measured by UMI counts", "zebrafish embryos", null, "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics  120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al.  2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen  37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics  120237 following the manufacture\u2019s introduction.", null, "region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "GSM3402061", "GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq", "GSM3402061", null, "1", "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics  120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al.  2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen  37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM3402061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP162658", null, null, "171353A_zebrafish_HSC_mixture-2_S10_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-2_S10_L001_R2_001.fastq.gz", "fastq fastq", 27785082649.0, 92332127.0, "GSM3402061 r3", "0:150.50 1:150.43", "A:7841096067;C:4446010985;G:4651723884;T:10845511192;N:740521", 150, 150, null, null, 7841096067, 4446010985, 4651723884, 10845511192, 740521, "SRX4741349", "SRS3822681", "SRA784241", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.04331, 0.91411, 0.00615, 0.06569, 0.97445, 0.81811, 0.49279, 0.49519, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-09-26", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["49407"], "units": {}, "query_ms": 10.194694987148978}