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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
61654 SRR12899700 SRX9364744 SRS7586959 SRP288616 PRJNA672101 Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq] GSE160140 Transcriptome Analysis NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified. parent bioproject:PRJNA672094 pubmed:35245286   WT GSM4861218   tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf type WT The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by “FilterCells” function. A global scaling normalization method “LogNormalize” was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using “FindAllMarkers” function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster Retinal single cell suspension   Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.   cell type:Retinal single cell suspension|strain:AB|age:5 mpf type GSM4861218 GSM4861218: WT; Danio rerio; RNA Seq GSM4861218   1 Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides. GEO Accession:GSM4861218 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288616     WT-TTTACCCA_BKDL192540873-1a-AK4444_1.fq.gz WT-TTTACCCA_BKDL192540873-1a-AK4444_2.fq.gz fastq fastq 31557387300.0 105191291.0 GSM4861218 r4 0:150 1:150 A:8779167981;C:6070335814;G:7200941655;T:9506741847;N:200003 150 150     8779167981 6070335814 7200941655 9506741847 200003 SRX9364744 SRS7586959 SRA1147910 GEO College of Life Science and Technology, Huazhong University of Science and Technology 2 0.0 0.82059 0.0 0.12768 1.0 0.82363   0.5393 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2020-10-26 Adult Adult Eye Sensory System