run_metadata: 76530
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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| 76530 | SRR25007135 | SRX20762485 | SRS18050780 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T2 2 | GSM7507239 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:24hpf|geo loc name:missing|collection date:missing | T2 2 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:24hpf | GSM7507239 | GSM7507239: T2 2; Danio rerio; RNA Seq | GSM7507239 r1 | GSM7507239 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T2_2.R1.fq.gz T2_2.R2.fq.gz | fastq fastq | 14696199900.0 | 48987333.0 | GSM7507239 r1 | 0:150 1:150 | A:3735683721;C:3615176348;G:3714335362;T:3630926317;N:78152 | 150 | 150 | 3735683721 | 3615176348 | 3714335362 | 3630926317 | 78152 | SRX20762485 | SRS18050780 | SRA1661372 | henan normal university | henan normal university | 2 | 0.42139 | 0.57658 | 0.08829 | 0.1292 | 0.78831 | 0.75617 | 0.44949 | 0.45776 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |