run_metadata: 61518
This data as json
| 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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| 61518 | SRR12786068 | SRX9255326 | SRS7487528 | SRP286633 | PRJNA667863 | Genes related to microtubule functions were downregulated in sinhcaf mutant FG follicles and eggs | GSE159162 | Transcriptome Analysis | Transcriptome sequencing RNA seq analysis uncovered that 1238 genes were upregulated 923 genes were downregulated in sinhcaf mutant FG follicles compared to wild type FG follicles. Loss of sinhcaf in mature eggs resulted in upregulation of 904 genes and downregulation of 911 genes. Downregulated genes in sinhcaf mutant FG follicles and eggs were classified by gene ontology GO analysis then the top 30 GO terms with highest log10P values were screened out and at least two downregulated genes were included in each biological processes cellular components or molecular function term. Microtubules and microtubule based processes were included in the top 30 GO terms. Overall design: RNA sequencing was performed on five biological replicates for mature egg four biological replicates for FG follicle of wild type and sinhcaf mutant zebrafish. Each biological replicate was a pool of mature eggs or FG follicles from one female zebrafish. | pubmed:35532311 | Sample KO EGG 5 | GSM4820782 | source name:follicles|tissue:Ovary|stage of follicles:mature egg|genotype:sinhcaf / | Sample KO EGG 5 | Then these libraries were sequenced on the Illumina sequencing platform Illumina HiSeq X Ten and 150bp paired end reads were generated. Raw data raw reads were processed using Trimmomatic. The reads containing poly N and the low quality reads were removed to obtain the clean reads. These clean reads were mapped to reference genome using hisat2. FPKM value of each gene was calculated using cufflinks and the read counts of each gene were obtained by htseq count. Genome build: GRCz11 Supplementary files format and content: Txt file includes gene ID gene name and FPKM values for each Sample | follicles | Total RNA was extracted using the mirVana miRNA Isolation Kit Ambion following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer Agilent Technologies Santa Clara CA USA. The samples with RNA Integrity Number RIN ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit Illumina San Diego CA USA according to the manufacturer’s instructions. | tissue:Ovary|stage of follicles:mature egg|genotype:sinhcaf / | GSM4820782 | GSM4820782: Sample KO EGG 5; Danio rerio; RNA Seq | GSM4820782 | 1 | Total RNA was extracted using the mirVana miRNA Isolation Kit Ambion following the manufacturer's protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer Agilent Technologies Santa Clara CA USA. The samples with RNA Integrity Number RIN ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit Illumina San Diego CA USA according to the manufacturer's instructions. | GEO Accession:GSM4820782 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP286633 | Sample_KO_EGG_5.R1.fq.gz Sample_KO_EGG_5.R2.fq.gz | fastq fastq | 6749303222.0 | 23750320.0 | GSM4820782 r1 | 0:142.69 1:141.49 | A:1797588338;C:1567936329;G:1570091501;T:1813621345;N:65709 | 142 | 141 | 1797588338 | 1567936329 | 1570091501 | 1813621345 | 65709 | SRX9255326 | SRS7487528 | SRA1139682 | GEO | Institute of Hydrobiology | 2 | 0.93455 | 0.9383 | 0.03024 | 0.02992 | 0.80511 | 0.80509 | 0.50954 | 0.49961 | 122 | 106 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | trueseq | bulk | unknown | unknown | China | 2020-10-07 | Undetermined | Undetermined | Gonad | Reproductive System |