run_metadata: 26482
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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| 26482 | SRR25930974 | SRX21649989 | SRS18818461 | SRP458853 | PRJNA1013567 | scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts | GSE242483 | Transcriptome Analysis | Seeking to identify additional transcription factors required for cardiac valve formation we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established and at 80 hpf when forming valves are first observed | pubmed:38748804 | 80hpf | GSM7764482 | source name:heart|tissue:heart|genotype:wild type|age:80hpf|geo loc name:missing|collection date:missing | 80hpf | Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs | heart | Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics. scRNA seq library preparation was done using a standard protocol and sequencing was done on a Nextseq2000 | tissue:heart|genotype:wild type|age:80hpf | GSM7764482 | GSM7764482: 80hpf; Danio rerio; RNA Seq | GSM7764482 r1 | GSM7764482 | 1 | Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics. scRNA seq library preparation was done using a standard protocol and sequencing was done on a Nextseq2000 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP458853 | Giulia_80hpf_S2_R1_001.fastq.gz Giulia_80hpf_S2_R2_001.fastq.gz | fastq fastq | 18811433188.0 | 225273324.0 | GSM7764482 r1 | 0:28 1:55.50 | A:5135587480;C:4020079745;G:4129712330;T:5427444755;N:98608878 | 28 | 55 | 5135587480 | 4020079745 | 4129712330 | 5427444755 | 98608878 | SRX21649989 | SRS18818461 | SRA1706674 | Bioinformatics, Max-Planck-Institute for Heart and Lung Research | Bioinformatics, Max-Planck-Institute for Heart and Lung Research | 2 | 0.00187 | 0.93611 | 0.00071 | 0.16105 | 0.99626 | 0.79825 | 0.41545 | 0.50249 | 28 | 55 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-09-06 | Larval | Larval | Heart | Cardiovascular System |