run_metadata: 72589
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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| 72589 | SRR22838795 | SRX18797976 | SRS16231609 | SRP414185 | PRJNA914428 | Single cell RNA sequencing scRNA seq of GFP+cells isolated from TgBrn3c:mGFP 6 days zebrafish with GFP expression in all hair cells. | GSE221471 | Other | Hair cells play key roles in hearing and balance and hair cell loss would result in hearing loss or vestibular dysfunction. Zebrafsh owing to their hair cell enriched organs have been widely applied in hair cell related research worldwide. In this study we analyzed the GFP+cells isolated from TgBrn3c:mGFP larvae with GFP expression in all hair cells using single cell RNA sequencing scRNA seq. Three subtypes of hair cells namely macula hair cell MHC crista hair cell CHC and neuromast hair cell NHC were characterized and validated by whole mount in situ hybridization analysis of marker genes. The hair cell scRNA seq data revealed hair cell specifc genes including hearing loss genes that have been identifed in humans and novel genes potentially involved in hair cell formation and function. Overall design: Zebrafsh were maintained at 28.5 °C. The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform | pubmed:35753015 | GFP+ scRNAseq | GSM6873779 | tissue:GFP+cells from TgBrn3c:mGFP zebrafish|cell type:hair cell|age:6 days | GFP+ scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: FASTQ | GFP+cells from TgBrn3c:mGFP zebrafish | The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | cell type:hair cell|age:6 days | GSM6873779 | GSM6873779: GFP+ scRNAseq; Danio rerio; RNA Seq | GSM6873779 r1 | GSM6873779 | 1 | The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP414185 | brn3c6dpf_R1.fq.gz brn3c6dpf_R2.fq.gz | fastq fastq | 201407352000.0 | 671357840.0 | GSM6873779 r1 | 0:150 1:150 | A:47653455771;C:37496314066;G:61110504409;T:55144480424;N:2597330 | 150 | 150 | 47653455771 | 37496314066 | 61110504409 | 55144480424 | 2597330 | SRX18797976 | SRS16231609 | SRA1563296 | Nantong University | Nantong University | 2 | 0.0 | 0.90004 | 0.0 | 0.18176 | 1.0 | 0.76794 | 0.55523 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | China | 2022-12-20 | Larval | Larval | Undetermined | Undetermined |