run_metadata: 66847
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| 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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| 66847 | SRR16681976 | SRX12882564 | SRS10825216 | SRP344071 | PRJNA776888 | Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts | GSE186957 | Transcriptome Analysis | Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish | pubmed:39741296 | runx2b+/+ scRNA seq | GSM5664292 | source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type | runx2b+/+ scRNA seq | Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample | muscle and IB | tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system. | strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type | GSM5664292 | GSM5664292: runx2b+/+ scRNA seq; Danio rerio; RNA Seq | GSM5664292 | 1 | tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system. | GEO Accession:GSM5664292 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP344071 | loader:fastq load.py|options: doNotUseSharq | WT_S1_L003_R1_001.fastq WT_S1_L003_R2_001.fastq | fastq fastq | 99838157100.0 | 332793857.0 | GSM5664292 r1 | 0:150 1:150 | A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720 | 150 | 150 | 30283010374 | 15529232903 | 16181518775 | 37842782328 | 1612720 | SRX12882564 | SRS10825216 | SRA1320685 | GEO | huazhong agricultural university | 2 | 0.34316 | 0.92608 | 0.04623 | 0.09467 | 0.98701 | 0.83644 | 0.72084 | 0.76059 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | illumina | novaseq_era | unknown | small_rna | trueseq | sc | single_cell_droplet | 10x | China | 2021-11-01 | Juvenile | Juvenile | Muscle | Muscular System |