run_metadata: 29196
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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| 29196 | SRR27308238 | SRX22985576 | SRS19950786 | SRP479308 | PRJNA1055256 | Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish | GSE251757 | Transcriptome Analysis | Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts. | pubmed:38193362 | EGFP+/sp7 CMP rep1 | GSM7987443 | source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing | EGFP+/sp7 CMP rep1 | High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. | 14 dpa adult caudal fin | Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. | Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. | tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry | GSM7987443 | GSM7987443: EGFP+/sp7 CMP rep1; Danio rerio; RNA Seq | GSM7987443 r1 | GSM7987443 | 1 | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP479308 | Mes-G_S15_R1_001.fastq.gz Mes-G_S15_R2_001.fastq.gz | fastq fastq | 5321588000.0 | 13303970.0 | GSM7987443 r1 | 0:200 1:200 | A:1405233304;C:1195662643;G:1342003810;T:1376732727;N:1955516 | 200 | 200 | 1405233304 | 1195662643 | 1342003810 | 1376732727 | 1955516 | SRX22985576 | SRS19950786 | SRA1773396 | Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology | Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology | 2 | 0.00961 | 0.02419 | 0.00032 | 0.00052 | 0.9945 | 0.99324 | 0.51073 | 0.48429 | 200 | 200 | T | T | mates < 9% mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2023-12-20 | Adult | Adult | Fin | Surface Structure |