{"database": "metadata", "table": "run_metadata", "rows": [[28483, "SRR26266493", "SRX21975998", "SRS19051834", "SRP464334", "PRJNA1023540", "ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling", "GSE244550", "Transcriptome Analysis", "Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with A\u00df42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to A\u00df42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data", null, "pubmed:39216475", null, "telencephalon  abca7 k/o   Ab42 injected", "GSM7819018", null, "source name:telencephalon|tissue:telencephalon|genotype:abca7 +/ |treatment:Ab42|geo loc name:missing|collection date:missing", "telencephalon  abca7 k/o   Ab42 injected", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger", "telencephalon", "WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.", "Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", "Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28\u00b0C \u00b11\u00b0C in groups of 20 animals per 2.8L.", "tissue:telencephalon|genotype:abca7 +/ |treatment:Ab42", "GSM7819018", "GSM7819018: telencephalon  abca7 k/o   Ab42 injected; Danio rerio; RNA Seq", "GSM7819018 r1", "GSM7819018", "1", "Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP464334", null, "loader:fastq load.py", "CP021_S12_L002_I1_001.fastq.gz CP021_S12_L002_I2_001.fastq.gz CP021_S12_L002_R1_001.fastq.gz CP021_S12_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 47673315186.0, 214744663.0, "GSM7819018 r2", "0:10 1:10 2:101 3:101", "A:12499321052;C:7231866994;G:7443419880;T:16203206561;N:607439", 10, 10, 101, 101, 12499321052, 7231866994, 7443419880, 16203206561, 607439, "SRX21975998", "SRS19051834", "SRA1725563", "Neurology & TAUB Institute, Columbia University", "Neurology & TAUB Institute, Columbia University", 2, 0.00305, 0.89832, 0.00064, 0.26179, 0.99851, 0.73434, 0.53932, 0.50016, 101, 101, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-10-03", "Undetermined", "Undetermined", "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": ["28483"], "units": {}, "query_ms": 8.851562000927515}