{"database": "metadata", "table": "run_metadata", "rows": [[30584, "SRR27848825", "SRX23511742", "SRS20362210", "SRP487850", "PRJNA1072679", "Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 2", "GSM8061003", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 2", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061003", "GSM8061003: Choroideremia 2; Danio rerio; RNA Seq", "GSM8061003 r1", "GSM8061003", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM2_1.fq.gz CHM2_2.fq.gz", "fastq fastq", 14968884300.0, 49896281.0, "GSM8061003 r1", "0:150 1:150", "A:4575866591;C:2606132581;G:2819446784;T:4967389772;N:48572", 150, 150, null, null, 4575866591, 2606132581, 2819446784, 4967389772, 48572, "SRX23511742", "SRS20362210", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.88022, 0.87326, 0.29312, 0.29812, 0.7335, 0.76228, 0.5854, 0.57614, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory 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": ["30584"], "units": {}, "query_ms": 9.666728001320735}