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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
28795 SRR26685984 SRX22385776 SRS19431938 SRP470412 PRJNA1036238 RNAseq of Wild Type and pikfyve?8 zebrafish. GSE247110 Transcriptome Analysis Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.       pikfyve2 GSM7883487   source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing pikfyve2 Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample genotype   The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing   tissue:genotype|genotype:pikfyve delta8 GSM7883487 GSM7883487: pikfyve2; Danio rerio; RNA Seq GSM7883487 r1 GSM7883487 1 The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP470412     pikfyve2_1.fq.gz pikfyve2_2.fq.gz fastq fastq 6640406100.0 22134687.0 GSM7883487 r1 0:150 1:150 A:1765647548;C:1547424271;G:1541609810;T:1785639698;N:84773 150 150     1765647548 1547424271 1541609810 1785639698 84773 SRX22385776 SRS19431938 SRA1746433 The Second Clinical Medical College, Jinan University The Second Clinical Medical College, Jinan University 2 0.93535 0.92946 0.08654 0.08582 0.67127 0.67298 0.48517 0.48183 150 150 B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-11-06 Undetermined Undetermined Undetermined Undetermined