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Sample GSM3097918 Query DataSets for GSM3097918
Status Public on Jul 26, 2018
Title TGBS_HRCS_rep1
Sample type SRA
 
Source name Spermatozoa
Organism Mus musculus
Characteristics sperm fraction: HRCS
strain: C57BL/6
dna selection: SureSelect (Agilent)
Treatment protocol After mild sonication to separate sperm head from the tail, HRCS (Histone Replacement- Complete Sperm) was isolated from total sperm fraction by 82% Percoll precipitation.
Growth protocol Caudal epididymis and vas deferens were incubated in M2 medium for 1 hour at 37C to prepare total sperm fraction.
Extracted molecule genomic DNA
Extraction protocol After treatment of sperm lysis buffer, genomic DNA was extracted from each sperm sample. DNA is purified by RNase and pronaseK treatment, and extracted by PCI separation and EtOH precipitation.
Libraries for targeted methylome sequencing were prepared according to the post-bisulfite adaptor tagging (PBAT) protocol (Miura F et al., 2012; Miura F and Ito T, 2015) with slight modifications. Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent). The enriched DNA was subjected to PBAT followed by 5 cycles of PCR enrichment with Kapa Library Amplification Kit. Single-read sequencing (100 cycles) was performed on Illumina HiSeq 2500 using HiSeq SR Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2. Two indexed libraries were combined with a high concentration of spike-in PhiX control DNA (20%) and loaded on a single lane of the flow cell.
Target BS-seq
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.4 software used for basecalling.
Targeted methylome sequencing reads were mapped to the mouse reference genome sequence (mm9) using Bmap (http://itolab.med.kyushu-u.ac.jp/BMap/index.html).
Methylation levels were calculated for individual CG sites.
Genome_build: mm9
Supplementary_files_format_and_content: BED files include chrmosome, position, strand, the number of mC reads and the number of total reads.
 
Submission date Apr 13, 2018
Last update date Jul 26, 2018
Contact name Hiromitsu Araki
E-mail(s) araki.hiromitsu.596@m.kyushu-u.ac.jp
Organization name Kyushu University
Street address 744 Motooka Nishi-Ku
City Fukuoka
ZIP/Postal code 819-0395
Country Japan
 
Platform ID GPL17021
Series (2)
GSE113137 DNA methylation analysis for target regions in swim-up sperm and HRCS.
GSE113150 Mapping of histone-binding sites in histone replacement-completed spermatozoa
Relations
BioSample SAMN08930495
SRA SRX3934597

Supplementary file Size Download File type/resource
GSM3097918_SH_WT1_S1_cpg.bed.gz 147.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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