{"database": "metadata", "table": "run_metadata", "rows": [[29824, "SRR27499206", "SRX23170203", "SRS20119600", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 17", "GSM8012744", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 17", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012744", "GSM8012744: non syn 17; Danio rerio; RNA Seq", "GSM8012744 r1", "GSM8012744", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-17_S1_L001_R1_001.fastq.gz non-syn-17_S1_L001_R2_001.fastq.gz", "fastq fastq", 1902575700.0, 6341919.0, "GSM8012744 r1", "0:150 1:150", "A:523356732;C:311424242;G:413587608;T:654191534;N:15584", 150, 150, null, null, 523356732, 311424242, 413587608, 654191534, 15584, "SRX23170203", "SRS20119600", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "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": ["29824"], "units": {}, "query_ms": 8.269721001852304}