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Sample GSM5531110 Query DataSets for GSM5531110
Status Public on Apr 24, 2024
Title gpSSCs-bulkATACseq-cko-rep1
Sample type SRA
 
Source name growth plate
Organism Mus musculus
Characteristics cre line: Prx-Cre
genotype: PrxCre; Z24fl/fl
age: 20-week-old
Extracted molecule genomic DNA
Extraction protocol For scRNA-seq, td-Tomato+ cells were isolated from bone marrow and bone by flow cytometry. For RNA-seq and ATAC-seq, td-Tomato+ cells were isolated from growth plate or periosteum by flow cytometry, and 1000 of these cells were used for constructing RNA-seq library, while 3000~5000 of these cells were used for constructing ATAC-seq library.
RNA-seq libraries were constructed by a modified Smartseq2 method with UMI barcodes (Nature 533:487, 2016). ATAC-seq libraries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 mouse genome using STAR (for RNA-seq) and Bowtie2 (for ATAC-seq).
For RNA-seq data, aligned reads with high quality were quantified by HTSeq. For ATAC-seq, reads mapped to mitochondrial DNA, with duplication or unknown identities were eliminated by Sambamba. Only unique reads were analyzed.
For RNA-seq data, counts per million reads (CPM) were calculated. For ATAC-seq, we performed peak calling using MACS2, summarized the read counts by bedtools and obtained the differential peaks by DESeq2.
For RNA-seq data, unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count file. For ATAC-seq, motif enrichment was performed by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq data, we provided tab-delimited text files including raw count values for each sample. For ATAC-seq data, we provided tab-delimited text files and binary files including all peaks.
 
Submission date Aug 21, 2021
Last update date Apr 24, 2024
Contact name Dandan Cao
E-mail(s) 1931465@tongji.edu.cn
Phone 17853136996
Organization name Tongji University
Street address 1239 Siping Road, Yangpu District
City Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL24247
Series (1)
GSE182540 Premature aging in growth-plate and periosteum resident skeletal stem cells is responsible for bone loss
Relations
BioSample SAMN20924234
SRA SRX11857678

Supplementary file Size Download File type/resource
GSM5531110_1-ZWG-gp-ko.bw 103.1 Mb (ftp)(http) BW
GSM5531110_1-ZWG-gp-ko_peaks.xls.gz 2.2 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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