{"database": "metadata", "table": "run_metadata", "rows": [[25105, "SRR25567717", "SRX21296458", "SRS18545736", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 1  RNAseq", "GSM7696243", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696243", "GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696243 r1", "GSM7696243", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "410-Tie1-WT-HT1_S1_L003_R1_001.fastq.gz", "fastq", 419693128.0, 5522278.0, "GSM7696243 r3", "0:76", "A:131491219;C:78551884;G:78434940;T:131179828;N:35257", 76, null, null, null, 131491219, 78551884, 78434940, 131179828, 35257, "SRX21296458", "SRS18545736", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.79077, null, 0.52836, null, 0.73419, null, 0.48215, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "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": ["25105"], "units": {}, "query_ms": 8.165384992025793}