run_metadata: 61645
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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 |
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| 61645 | SRR12899694 | SRX9364741 | SRS7586956 | SRP288615 | PRJNA672100 | Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq] | GSE160138 | 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: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified. | parent bioproject:PRJNA672094 | pubmed:35245286 | WT R2 | GSM4861207 | source name:Retina|tissue:Retina|strain:AB|age:2 mpf type | WT R2 | Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes | Retina | For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol. | tissue:Retina|strain:AB|age:2 mpf type | GSM4861207 | GSM4861207: WT R2; Danio rerio; RNA Seq | GSM4861207 | 1 | For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol. | GEO Accession:GSM4861207 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP288615 | WT-R2_combined_R1.fastq.gz WT-R2_combined_R2.fastq.gz | fastq fastq | 7066558200.0 | 23555194.0 | GSM4861207 r1 | 0:150 1:150 | A:1911018201;C:1615965707;G:1630234641;T:1909071420;N:268231 | 150 | 150 | 1911018201 | 1615965707 | 1630234641 | 1909071420 | 268231 | SRX9364741 | SRS7586956 | SRA1147909 | GEO | College of Life Science and Technology, Huazhong University of Science and Technology | 2 | 0.91673 | 0.91647 | 0.11542 | 0.11684 | 0.68781 | 0.69637 | 0.48784 | 0.49134 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | sc_generic | bulk | bulk | China | 2020-10-26 | Juvenile | Juvenile | Eye | Sensory System |