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Sample GSM1206692 Query DataSets for GSM1206692
Status Public on Dec 02, 2013
Title WT-1 PGC
Sample type SRA
 
Source name WT_E13.5 PGC
Organism Mus musculus
Characteristics strain background: C57BL/6J
genotype/variation: wild type
tissue: primordial germ cells (PGCs)
Extracted molecule genomic DNA
Extraction protocol DNA was extracted in DNA lysis buffer (10 mM Tris-HCl (pH 8.5), 10 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 mg/ml proteinase K followed by phenol:chloroform extraction and ethanol precipitation.
DNA was digested with MspI (NEB), and then subjected to end repair, and ligation of methylated custom adaptors (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where * indicates phosphorothioate bond) with a NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Size selection was conducted by purifying the adaptor-ligated DNA twice with 1.5× SPRIselect beads (Beckman Coulter). Size selected libraries were treated with sodium bisulfite using the EpiTect Fast Bisulfite Conversion Kit (QIAGEN). After clean-up, the optimal, minimum PCR cycle numbers required to generate the final libraries were determined by qPCR using KAPA 2G Robust HotStart ReadyMix (KAPA) with 0.3× SYBR I. Final libraries were generated by scaled-up PCR reactions (without SYBR I) using the cycles determined above with barcoded primers from NEBNext Multiplex Oligos kit (NEB), and purified with 1.2× SPRIselect beads.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Bcl2fastq 1.8.2 software was used for demultiplexing and generation of fastq files
Adapter trimming for all reads from each sample was performed using Trim Galore (Babraham Bioinformatics)
The trimmed reads were mapped against the mouse genome (mm9 build) with Bismark v0.7.12, and the methylation call for every single C was extracted by bismark methylation extractor script. All programs were performed with default setting.
Genome_build: mm9
Supplementary_files_format_and_content: summarized methylation percentage (single-base resolution)
 
Submission date Aug 11, 2013
Last update date May 15, 2019
Contact name Li Shen
Organization name HHMI/Boston Children's Hospital/Harvard Medical School
Street address 200 Longwood Ave
City Boston
ZIP/Postal code 02115
Country USA
 
Platform ID GPL17021
Series (2)
GSE49762 Role of Tet1 in genomic imprinting erasure [RRBS-PGC]
GSE49764 Role of Tet1 in genomic imprinting erasure
Relations
BioSample SAMN02315361
SRA SRX333430

Supplementary file Size Download File type/resource
GSM1206692_RRBS4PGC_WT1_ratio.bedGraph.gz 2.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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