RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata: 25128

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
25128 SRR25610725 SRX21337839 SRS18583008 SRP454647 PRJNA1004574 Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf GSE240655 Transcriptome Analysis Melanocytes of the skin have traditionally been viewed as a homogeneous population however recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study we utilized a transgenic zebrafish line Tgmifa:GFP that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter mitfa labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer parent bioproject:PRJNA975369 pubmed:39163475   mitfa low zf scRNAseq GSM7706846   tissue:mitfa:GFP+ cells|genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP low|age:24 hpf loc name:missing|collection date:missing mitfa low zf scRNAseq The demultiplexing barcode processing gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files mitfa:GFP+ cells   Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter’s instructions single cell 3’ v3.1 single index protocol 10x Genomics. Briefly 24hpf mitfa:GFP low and high zebrafish cells 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 sample index were added.   genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP low|age:24 hpf GSM7706846 GSM7706846: mitfa low zf scRNAseq; Danio rerio; RNA Seq GSM7706846 r1 GSM7706846 1 Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol 10x Genomics. Briefly 24hpf mitfa:GFP low and high zebrafish cells 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 sample index were added.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP454647   loader:fastq load.py LM_S3_L001_R2_001.fastq.gz LM_S3_L001_R1_001.fastq.gz LM_S3_L001_I1_001.fastq.gz fastq fastq fastq 17519211850.0 137946550.0 GSM7706846 r1 0:8 1:28 2:91 A:3674575574;C:2564940740;G:3313017210;T:3000585838;N:16688 8 28 91   3674575574 2564940740 3313017210 3000585838 16688 SRX21337839 SRS18583008 SRA1691286 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB 1 0.81163   0.13698   0.859   0.52032   91   B   usable mapping rate illumina nextseq_v2 unknown poly_a unknown sc single_cell_droplet 10x   India 2023-08-11 Pharyngula Embryo Embryo Imprecise All anatomical structures