run_metadata: 54734
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 54734 | SRR10150443 | SRX6875866 | SRS5411730 | SRP222654 | PRJNA571187 | single cell RNA Seq of juvenile zebrafish | PRJNA571187 | Other | single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit | whole organism single cell RNA seq of juvenile zebrafish | SC2S3 | strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal | single cell RNA Seq of zebrafish: whole organism of juvenile | I1S1 | I1S1 | A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | HiSeq X Ten | SRP222654 | S3-I1-Hiseq_S1_L001_R1_001.fastq.gz S3-I1-Hiseq_S1_L001_R2_001.fastq.gz | fastq fastq | 7809763800.0 | 26032546.0 | S3 I1 Hiseq S1 L001 R1 001.fastq.gz | 0:150 1:150 | A:1991021603;C:1400155384;G:1489635110;T:2928896892;N:54811 | 150 | 150 | 1991021603 | 1400155384 | 1489635110 | 2928896892 | 54811 | SRX6875866 | SRS5411730 | SRA965192 | Sun Yat- sen University|Life Sicence School | Sun Yat- sen University | 2 | 0.06891 | 0.85095 | 0.01881 | 0.14251 | 0.98555 | 0.78772 | 0.49154 | 0.57233 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | China | 2019-09-20 | Juvenile | Juvenile | Whole Organism | All anatomical structures |