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Status |
Public on Dec 02, 2013 |
Title |
WT-1 PGC |
Sample type |
SRA |
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Source name |
WT_E13.5 PGC
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Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6J genotype/variation: wild type tissue: primordial germ cells (PGCs)
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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.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
Reduced Representation |
Instrument model |
Illumina HiSeq 2500 |
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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)
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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
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Street address |
200 Longwood Ave
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City |
Boston |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (2) |
GSE49762 |
Role of Tet1 in genomic imprinting erasure [RRBS-PGC] |
GSE49764 |
Role of Tet1 in genomic imprinting erasure |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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