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GEO help: Mouse over screen elements for information. |
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Status |
Public on Apr 24, 2024 |
Title |
gpSSCs-bulkATACseq-cko-rep1 |
Sample type |
SRA |
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Source name |
growth plate
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Organism |
Mus musculus |
Characteristics |
cre line: Prx-Cre genotype: PrxCre; Z24fl/fl age: 20-week-old
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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).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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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.
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Submission date |
Aug 21, 2021 |
Last update date |
Apr 24, 2024 |
Contact name |
Dandan Cao |
E-mail(s) |
1931465@tongji.edu.cn
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Phone |
17853136996
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Organization name |
Tongji University
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Street address |
1239 Siping Road, Yangpu District
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City |
Shanghai |
ZIP/Postal code |
200092 |
Country |
China |
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Platform ID |
GPL24247 |
Series (1) |
GSE182540 |
Premature aging in growth-plate and periosteum resident skeletal stem cells is responsible for bone loss |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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