run_metadata: 50528
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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| 50528 | SRR8129709 | SRX4950831 | SRS3993022 | SRP167139 | PRJNA499073 | Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes | GSE121917 | Transcriptome Analysis | We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo. | pubmed:30894119 | RNAqueous unsorted | GSM3449970 | tissue:Fli:GFP whole embryo 5 days RNAqueous sample 1|cell type:fli:GFP whole embryo|age:5 days|rna isolation kit:RNAqueous micro | RNAqueous unsorted | Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data | Fli:GFP whole embryo 5 days RNAqueous sample 1 | polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina | cell type:fli:GFP whole embryo|age:5 days|rna isolation kit:RNAqueous micro | GSM3449970 | GSM3449970: RNAqueous unsorted; Danio rerio; RNA Seq | GSM3449970 | 1 | polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina | GEO Accession:GSM3449970 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP167139 | A_unsorted_R1.fastq.gz A_unsorted_R2.fastq.gz | fastq fastq | 3613198121.0 | 23920751.0 | GSM3449970 r1 | 0:75.53 1:75.52 | A:976322858;C:832409562;G:835538411;T:968916959;N:10331 | 75 | 75 | 976322858 | 832409562 | 835538411 | 968916959 | 10331 | SRX4950831 | SRS3993022 | SRA800291 | GEO | Center for Medical Genetics, Ghent University | 2 | 0.91518 | 0.91772 | 0.12399 | 0.12715 | 0.71196 | 0.71764 | 0.46555 | 0.45805 | 72 | 75 | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | nextera | sc | single_cell_plate | smartseq | Belgium | 2018-10-29 | Larval | Larval | Whole Organism | All anatomical structures |