{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE183nnn/GSE183543/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Mus musculus"],"gds_type":[" Genome binding/occupancy profiling by high throughput sequencing","Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183543"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Next Generation Sequencing Facilitates Quantitative Analysis of transcriptome and epigenome in skeletal stem cell sorted from Ptipfl/fl and Ptipf/f;Col2-Cre mice","description":"Purpose: the goals of this study are to map epigenetic alterations drive the trajectory of skeletal stem and progenitor cells by integrating their cis-regulatory landscape(ChIP-seq) with the transcriptomic profiling(RNA-seq) Methods: freshly sorted SSCs, pBCSPs, and BCSPs by FACS (Fluorescence activated Cell Sorting) from 3-day-old Ptipf/f mice and conditional knockout Ptip by crossing col2a1-cre mice and Ptipfl/fl mice (Ptipf/f;Col2-Cre mice) were performed RNA-seq and ChIP-seq (H3K4me1/H3K4me3/H3K27ac-ChIPseq). Results: using an optimized data analysis workflow, we integrated their cis-regulatory landscape with the transcriptomic profiling. As expected, expression levels of genes were associated with the activity of their related cis-regulatory elements in SSCs, pBCSPs and BCSPs. Conclusions: Ptip play a crucial role in epigenetic alterations governing the developmental trajectory of skeletal stem and progenitor cells.","dates":{"publication":"2024/09/06"},"accession":"GSE183543","cross_references":{"GSM":["GSM5560152","GSM5560173","GSM5560151","GSM5560172","GSM5560150","GSM5560171","GSM5560156","GSM5560155","GSM5560154","GSM5560153","GSM5560138","GSM5560159","GSM5560158","GSM5560157","GSM5560139","GSM5903582","GSM5903581","GSM5903580","GSM5903586","GSM5903585","GSM5903584","GSM5903583","GSM5560170","GSM5903589","GSM5903588","GSM5903587","GSM5560141","GSM5560163","GSM5560162","GSM5560140","GSM5560161","GSM5560160","GSM5560167","GSM5560145","GSM5560144","GSM5560166","GSM5560165","GSM5560143","GSM5560164","GSM5560142","GSM5560149","GSM5560148","GSM5560147","GSM5560169","GSM5560168","GSM5560146","GSM5903591","GSM5903590"],"GPL":["24247"],"SRA":["SRP335921"],"GSE":["183543"],"taxon":["Mus musculus"],"PMID":["[38493069]"]}}