|
| Status |
Public on Oct 15, 2012 |
| Title |
PGK_1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type female embryonic stem cell line paired end 1
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wild type
gender: female
cell line: PGK
|
| Treatment protocol |
MEF cell lines were untreated. ES cell differentiation followed the standard embryoid body method.
|
| Growth protocol |
Standard culture conditions including 5% CO2, 37oC, 5% fetal calf serum, penicillin and streptomycin in DMEM culture media. For ES cell growth cells were maintained with 10% fetal calf serum and supplemented with LIF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated using a standard protocol after RNase and proteinase K treatment, it was then sonicated to between 200-600 bp, before 20-30 ug was fractionated using a MBD column. Unmethylated DNA was eluted with 0.715 M NaCl and methylated DNA with 1M NaCl. Efficient fractionation was confirmed by PCR analysis of fractions for known methylated and unmethylated loci. Methylated DNA was then pooled, concentrated, desalted in a 30K filter and precipitated. Samples were resuspended in 20 microlitres of H20 and submitted for sequencing after quality was confirmed using picogreen. Each sample isolation and MBD-seq was performed.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
solexa1.3 basecalling
mapping to genome with bowtie -m 1
conversion of sam/bam files to bigwig using bamToGBrowse.pl (http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.14/bin/bamToGBrowse.pl)
Genome_build: mm9
|
| |
|
| Submission date |
Apr 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Taylor |
| E-mail(s) |
stephen.taylor@imm.ox.ac.uk
|
| Phone |
+44 1865 222640
|
| Organization name |
CBRG
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE37333 |
Smchd1 dependent and independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome. |
|
| Relations |
| SRA |
SRX142897 |
| BioSample |
SAMN00857899 |
