|
| Status |
Public on Mar 04, 2010 |
| Title |
m_Cerebellum_MBD_M |
| Sample type |
SRA |
| |
|
| Source name |
Cerebellum
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 30 weeks
chip antibody / mbd affinity column: Methyl-seq (recombinant human MBD domain)
tissue: cerebellum
|
| Treatment protocol |
Cerebellum DNA was extracted according to standard protocols. DNA was sheared to approximately 400 bp using sonication. Methylated DNA was purified by two step MBD Affinity Purification as described in Illingworth et al., 2008.
|
| Growth protocol |
Whole brains / Cerebellum were disected from C57black/6 mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
MBD affinity chromatography
|
| Data processing |
Alignment: Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained.
|
| |
|
| Submission date |
Jan 07, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Adrian P Bird |
| E-mail(s) |
A.Bird@ed.ac.uk
|
| Phone |
0131 6508695
|
| Fax |
0131 6505379
|
| Organization name |
The University of Edinburgh
|
| Department |
WTCCB
|
| Lab |
Bird Lab
|
| Street address |
Mayfield Road
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE19786 |
Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state |
|
| Relations |
| SRA |
SRX017295 |
| BioSample |
SAMN00009569 |
