run_metadata: 59888
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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| 59888 | SRR12067712 | SRX8595501 | SRS6886082 | SRP268312 | PRJNA641114 | Single cell transcriptomic analysis 30 hpf Zebrafish trunks | GSE152982 | Other | Here we performed single cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified spanning all three embryonic germ layers. Overall design: Whole trunks excised from 30 embryos at 30 hpf were dissociated using a cold protease dissociation protocol. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform. | pubmed:34234366 | Zf 30h trunk | GSM4631066 | source name:Zebrafish Trunks|age:30 hpf|tissue:trunk|genotype:wildtype | Zf 30h trunk | All processing was performed in 10X Genomics CellRanger v3.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.11 and to obtain the gene expression matrices Genome build: GRCz11 Supplementary files format and content: mtx matrix files | Zebrafish Trunks | Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol | age:30 hpf|tissue:trunk|genotype:wildtype | GSM4631066 | GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq | GSM4631066 | 1 | Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol | GEO Accession:GSM4631066 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268312 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Zf30hTrunk S1 L002 I1 001.fastq.gz read2PairFiles=Zf30hTrunk S1 L002 R1 001.fastq.gz read3PairFiles=Zf30hTrunk S1 L002 R2 001.fastq.gz | Zf30hTrunk_S1_L002_I1_001.fastq.gz Zf30hTrunk_S1_L002_R1_001.fastq.gz Zf30hTrunk_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 31428372976.0 | 172683368.0 | GSM4631066 r2 | 0:8 1:27 2:147 | A:8978925123;C:6926043302;G:7091713953;T:8399543364;N:32147234 | 8 | 27 | 147 | 8978925123 | 6926043302 | 7091713953 | 8399543364 | 32147234 | SRX8595501 | SRS6886082 | SRA1089692 | GEO | University of South Florida | 1 | 0.87666 | 0.09235 | 0.85277 | 0.49776 | 147 | B | usable mapping rate | illumina | hiseq_era | 3prime | cdna_unspecified | nextera | sc | single_cell_droplet | 10x | United States | 2020-06-22 | Pharyngula | Embryo | Trunk | Surface Structure |