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Sample GSM5531086 Query DataSets for GSM5531086
Status Public on Apr 24, 2024
Title Prx1-Cre-scRNAseq
Sample type SRA
Source name bone marrow and bone
Organism Mus musculus
Characteristics cre line: Prx-Cre
genotype: PrxCre; Z24fl/fl
age: 8-week-old
Extracted molecule polyA RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
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
Phone 17853136996
Organization name Tongji University
Street address 同济大学四平校区
City 上海市
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
BioSample SAMN20924210
SRA SRX11857682

Supplementary file Size Download File type/resource
GSM5531086_Prx1-Cre-barcodes.tsv.gz 5.5 Kb (ftp)(http) TSV
GSM5531086_Prx1-Cre-features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM5531086_Prx1-Cre-matrix.mtx.gz 2.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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