|
| Status |
Public on Feb 14, 2013 |
| Title |
mBS47 |
| Sample type |
SRA |
| |
|
| Source name |
ESCs-Rosa26-GFP
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
lentivirus: No virus
cell type: ESCs-Rosa26-GFP
|
| 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 Genome Analyzer II |
| |
|
| 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 |
GPL9250 |
| Series (1) |
| GSE44092 |
Bisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs) |
|
| Relations |
| SRA |
SRX229525 |
| BioSample |
SAMN01915379 |
