run_metadata: 61425
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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| 61425 | SRR12749598 | SRX9221555 | SRS7455256 | SRP285948 | PRJNA666689 | Spatio temporal mRNA tracking in the early zebrafish embryo | GSE158849 | Other | We performed spatially resolved transcriptomics with sub single cell resolution in zebrafish embryos at the one cell stage which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac the vegetal pole. The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys mature X. laevis and X. tropicalis oocytes. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf. | pubmed:34099733 | scSLAM seq replicate 1 | GSM4812182 | tissue:shield stage embryos 6 hpf|strain:AB wildtype|treatment:4sUTP injected|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome. | scSLAM seq replicate 1 | zebrafish tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode Genome build: GRCz10 release 90 Supplementary files format and content: csv file containing gene counts per section xenopus tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode and translate gene identifier to gene names Genome build: X. tropicalis v9.1 genome assembly X.laevis v9.2 genome assembly Supplementary files format and content: csv file containing gene counts per section scSLAM seq zebrafish demultiplexing using cellranger mkfastq v3.0.2 mapping and whitelisting of cells with cellranger v3.0.2 splitting labeled reads >1 T C mutation from unlabeled into separate fastq files submitted to this GEO entry mapping with STARsolo v2.7.0f 0328 single cell analysis in seurat v3.1.2 Genome build: GRCz11 Supplementary files format and content: barcodes.tsv list of barcodes genes.tsv list of genes and matrix.tsv count matrix | shield stage embryos 6 hpf | none provided by the submitter | strain:AB wildtype|treatment:4sUTP injected|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome. | GSM4812182 | GSM4812182: scSLAM seq replicate 1; Danio rerio; RNA Seq | GSM4812182 | 1 | none provided by the submitter | GEO Accession:GSM4812182 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP285948 | scSLAMseq.zebrafish.6hpf.R1.fastq.gz scSLAMseq.zebrafish.6hpf.R2.fastq.gz | fastq fastq | 18763873688.0 | 151321562.0 | GSM4812182 r1 | 0:26 1:98 | A:5330726187;C:3994611684;G:4055930332;T:5373535151;N:9070334 | 26 | 98 | 5330726187 | 3994611684 | 4055930332 | 5373535151 | 9070334 | SRX9221555 | SRS7455256 | SRA1136461 | GEO | Junker, BIMSB, MDC | 2 | 0.00126 | 0.81459 | 0.0004 | 0.05503 | 0.99717 | 0.82674 | 0.52121 | 0.58038 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2020-09-30 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |