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Sample GSM1078334 Query DataSets for GSM1078334
Status Public on Feb 14, 2013
Title mBS56
Sample type SRA
 
Source name iPGCs-V6.5
Organism Mus musculus
Characteristics genotype: wild type
lentivirus: no virus
cell type: iPGCs-V6.5
Growth protocol ESCs were cultured under standard conditions in LIF on feeders. iPGCs were generated via ESC differentiation for 6 days following selection of SSEA1+/cKitbright cells by FACS. Indicated viruses were transduced into ESCs prior to embryoid body differentiation.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated via Zymo gDNA Mini Prep columns and subjected to sonication.
Briefly, sonicated DNA was end repaired with T4/Klenow DNA polymerases and T4 polynucleotide kinase, adenylated, and ligated to pre-methylated single end Illumina Adapters with T4 DNA ligase. Following purification and size selection (150-300bp), samples were bisulfite converted with CpG Genome Kit (Millipore). Libraries were then subjected to one round of PCR amplification (15 cycles)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing BS-seq reads were aligned to the mm9 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data (CGmap) is in text format. column 1=chromosome id (see mouse_mm9_chr_name_id.txt); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
 
Submission date Feb 05, 2013
Last update date May 15, 2019
Contact name John Vincent
E-mail(s) jvincent@ucla.edu
Organization name UCLA
Department MCDB
Street address 621 Charles E Young Dr. S
City Los Angeles
ZIP/Postal code 90095
Country USA
 
Platform ID GPL13112
Series (1)
GSE44092 Bisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs)
Relations
SRA SRX229530
BioSample SAMN01915384

Supplementary file Size Download File type/resource
GSM1078334_mBS56.CGmap.txt.gz 2.3 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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