{"database": "metadata", "table": "run_metadata", "rows": [[52802, "SRR9207161", "SRX5978246", "SRS4884501", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DN rep2", "GSM3855038", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected", "RNA seq Wt DN rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected", "GSM3855038", "GSM3855038: Wt DN rep2; Danio rerio; RNA Seq", "GSM3855038", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855038", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_252_1_pair.fq.gz WTCHG_236896_252_2_pair.fq.gz", "fastq fastq", 2146316233.0, 14628161.0, "GSM3855038 r1", "0:74.84 1:71.88", "A:566578244;C:489485503;G:504442873;T:585776104;N:33509", 74, 71, null, null, 566578244, 489485503, 504442873, 585776104, 33509, "SRX5978246", "SRS4884501", "SRA894667", "GEO", "Oxford University", 2, 0.94696, 0.79752, 0.10017, 0.0872, 0.74572, 0.78165, 0.50212, 0.49488, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular 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": ["52802"], "units": {}, "query_ms": 10.382868997112382}