{"database": "metadata", "table": "run_metadata", "rows": [[56883, "SRR11178131", "SRX7798810", "SRS6213687", "SRP250666", "PRJNA608660", "Expression analysis of adult zebrafish enteric nervous system", "GSE145885", "Transcriptome Analysis", "The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish  we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris  samples were centrifuged at 1000 x G for 10 min at 4\u00b0C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis  doublet discrimination gating was applied to exclude aggregated nuclei  and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry  non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate  sorted cells from an average of 30 adult guts were pooled  containing approximately 30 000 Cherry+ or Cherry  nuclear populations.", null, "pubmed:32851974", null, "Adult gut sox10:cre;Cherry negative 5", "GSM4338415", null, "source name:Adult gut sox10:cre;Cherry negative|tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA", "Adult gut sox10:cre;Cherry negative 5", "The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2  was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.", "Adult gut sox10:cre;Cherry negative", "Nuclei were purified by FACS fluorescent activated cell sorting  representing both the Cherry+ entire ENS and Cherry  non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut", "Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer\u2019s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.", "N/A", "tissue:adult gut|cell type:non ENS|rna fraction:Nuclear mRNA", "GSM4338415", "GSM4338415: Adult gut sox10:cre;Cherry negative 5; Danio rerio; RNA Seq", "GSM4338415", null, "1", "Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies  Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific  Inc.  and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris  Inc. at standard settings. The fragmented cDNA was then normalized to 100ng  which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies  Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies  Inc.. The libraries were then normalized to 4 nM  pooled and loaded onto a HiSeq4000 Illumina  Inc. to generate 100 bp paired end reads.", "GEO Accession:GSM4338415", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP250666", null, null, "PE_neg_5_R1.fastq.gz PE_neg_5_R2.fastq.gz", "fastq fastq", 7402006796.0, 36643598.0, "GSM4338415 r1", "0:101 1:101", "A:2141100609;C:1495392069;G:1539459100;T:2225819644;N:235374", 101, 101, null, null, 2141100609, 1495392069, 1539459100, 2225819644, 235374, "SRX7798810", "SRS6213687", "SRA1047946", "GEO", "Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute", 2, 0.79957, 0.80443, 0.53128, 0.53529, 0.74728, 0.75968, 0.53126, 0.55373, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2020-02-25", "Adult", "Adult", "Gut", "Digestive 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": ["56883"], "units": {}, "query_ms": 8.996147000289056}