{"database": "metadata", "table": "run_metadata", "rows": [[53605, "SRR9961221", "SRX6708754", "SRS5262469", "SRP218233", "PRJNA560048", "Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons", "GSE135781", "Transcriptome Analysis", "Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.", null, "pubmed:32302545", null, "9 RA", "GSM4029964", null, "tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede", "9 RA", "Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts", "Vagus motor neurons", "Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.", "The posterior hindbrain was manually dissected in calcium free Ringer\u2019s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2\uf06dg/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.", null, "cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede", "GSM4029964", "GSM4029964: 9 RA; Danio rerio; RNA Seq", "GSM4029964", null, "1", "The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2\uf06dg/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.", "GEO Accession:GSM4029964", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP218233", null, null, "9_RA.R1.fastq.gz 9_RA.R2.fastq.gz", "fastq fastq", 2752434100.0, 27524341.0, "GSM4029964 r1", "0:50 1:50", "A:742948333;C:630419013;G:638493678;T:739745278;N:827798", 50, 50, null, null, 742948333, 630419013, 638493678, 739745278, 827798, "SRX6708754", "SRS5262469", "SRA938976", "GEO", "Fred Hutchinson Cancer Research Center", 2, 0.91252, 0.91511, 0.0935, 0.09935, 0.7303, 0.73612, 0.48109, 0.47973, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-08-13", "Pharyngula", "Embryo", "Brain", "Nervous 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": ["53605"], "units": {}, "query_ms": 7.603412999742432}