{"database": "metadata", "table": "run_metadata", "rows": [[34154, "SRR31377593", "SRX26751156", "SRS23239769", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R5", "GSM8637008", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R5", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637008", "GSM8637008: CCSER1 S Body R5; Danio rerio; RNA Seq", "GSM8637008 r1", "GSM8637008", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW040_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW040_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3646264950.0, 12073725.0, "GSM8637008 r1", "0:151 1:151", "A:939260848;C:884661915;G:900614466;T:921376437;N:351284", 151, 151, null, null, 939260848, 884661915, 900614466, 921376437, 351284, "SRX26751156", "SRS23239769", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"]], "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": ["34154"], "units": {}, "query_ms": 10.453881011926569}