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Series GSE133515 Query DataSets for GSE133515
Status Public on Jun 04, 2020
Title Profiling of DNA Methylation during RANKL Induced Osteoclastogenesis using Whole-Genome Bisulfite Sequencing
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Purpose: The goals of this study are to describe the DNA methylation profile during RANKL induced osteoclastogenesis.
Methods: Primary bone marrow cells were isolated and treated with M-CSF (30ng/mL) to generate bone marrow macrophages (BMMs). BMMs were then used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more. DNA methylation profiles of BMM, pOC and mOC were generated by deep sequencing, using Illumina NovaSeq 6000.
Results: After acquiring of clean reads, we used Hisat2 for spliced mapping. We mapped about 40 million sequence reads per sample of the WGBS results. Saturation rate analysis was then performed evaluating the gene coverage rate along with read depth increase. The transcripts mapping to difference functional region of the genome was then analyzed. Circos software was used to map the consistency of samples with mouse genome on a chromosomal level. The quantification of transcript intensity was analyzed using RPKM (Reads Per Kb per Million reads).
Conclusions: Our study represents the first high-throughput WGBS sequencing data of DNA methylation during osteoclastogenesis.
Overall design DNA methylation of ostoeclast at distinct differentiation stages were determined using WGBS.
Contributor(s) Dou C, Ma Q
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Submission date Jun 28, 2019
Last update date Jun 04, 2020
Contact name Ce Dou
Phone +8613883443401
Organization name Third Military Medical University
Street address Gaotanyan Street No.30
City Chongqing
State/province Chongqing
ZIP/Postal code 400038
Country China
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM3911211 BMM
GSM3911212 pOC
GSM3911213 mOC
BioProject PRJNA551674
SRA SRP212622

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Supplementary file Size Download File type/resource
GSE133515_S0H_CX_report_txt_gzvsGSE133515_S24H_CX_report_txt_gz-final.xlsx 24.0 Mb (ftp)(http) XLSX
GSE133515_S0H_CX_report_txt_gzvsS72H_CX_report_txt_gz-final.xlsx 6.7 Mb (ftp)(http) XLSX
GSE133515_S24H_CX_report_txt_gzvsS72H_CX_report_txt_gz-final.xlsx 24.5 Mb (ftp)(http) XLSX
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