run_metadata: 66237
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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| 66237 | SRR16195511 | SRX12479999 | SRS10443549 | SRP339965 | PRJNA768450 | Time resolved RNA sequencing reveals distinct post transcriptional regimes during zebrafish embryogenesis | GSE185283 | Other | We report the characterization of transcript dynamics during maternal to zygotic transition in Zebrafish MZT using thiol linked alkylation for the metabolic sequencing of RNA SLAMseq. Overall design: Quantification of de novo transcription during MZT | pubmed:36757845 | Fertilized oocyte replicate 2 Fertilized oocyte 2 | GSM5610103 | tissue:Zebrafish oocytes|cell type:oocyte|strain:TLAB TL X AB|chip antibody:3 prime end sequencing|treatment:Untreated | Fertilized oocyte replicate 2 Fertilized oocyte 2 | three prime end sequencing data were used to creat custom annotations using three prime GAmES SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome Additional SNP filtering was performed using samtools pileup TTSLAMseq data were sequentially mapped to rRNA sequences mitochondrial sequences and then the genome. other RNAseq data were mapped to dr11 using STAR and counted using featureCounts Genome build: dr11 Supplementary files format and content: count files of SLAMseq data were created using custom scripts post SNP filtering Supplementary files format and content: bedgraph files were genererated using deeptools Supplementary files format and content: Count files of TTSLAmseq data were obtained from SLAMdunk | Zebrafish oocytes | Zebrafish embryos were injected with 4sU or incubated in 4sU | QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs. | Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14 hour light/10 hour dark cycle. TLAB fish were generated by crossing zebrafish AB and the natural variant TL Tupfel Longfin stocks and used for all experiments. | cell type:oocyte|strain:TLAB TL X AB|chip antibody:3 prime end sequencing|treatment:Untreated | GSM5610103 | GSM5610103: Fertilized oocyte replicate 2 Fertilized oocyte 2; Danio rerio; RNA Seq | GSM5610103 | 1 | QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs. | GEO Accession:GSM5610103 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP339965 | WT_Ooc_FER_R2.fastq.gz | fastq | 727606300.0 | 7276063.0 | GSM5610103 r1 | 0:100 | A:255161621;C:130820008;G:159259242;T:182321712;N:43717 | 100 | 255161621 | 130820008 | 159259242 | 182321712 | 43717 | SRX12479999 | SRS10443549 | SRA1305700 | GEO | Institute of Molecular Biotechnology | 1 | 0.60979 | 0.06401 | 0.83871 | 0.58404 | 100 | B | usable mapping rate | illumina | hiseq_era | 3prime | cdna_unspecified | nebnext | bulk | unknown | unknown | Austria | 2021-10-04 | Zygote | Embryo | Oocyte | Reproductive System |