|
| Status |
Public on Jan 01, 2014 |
| Title |
02_CP1 |
| Sample type |
SRA |
| |
|
| Source name |
manually dissected E16 CP tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
developmental stage: E16
tissue: CP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Methylated DNA was purified with Methylated DNA Enrichment Kit (Clontech) and was subjected to library construction by ChIP-Seq Sample Prep Kit (Illumina) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
manually dissected E16 CP tissue
The ventricular zone (VZ) is enriched in neuronal progenitor, while the cortical plate (CP) is enriched in differentiating neurons.
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequence reads were mapped on the mouse genome assembly (NCBI37/mm9) with Bowtie mapping software
Enriched area was detected with Model-based analysis of ChIP-Seq (MACS)
gsize=1870000000 and mfold=10,30 were used for MACS parameter
Genome_build: mm9
Supplementary_files_format_and_content: xls file contains the following information: Region_name, Position, Length, Fold enrichment, Gene ID, and distance from gene body
"CP-cont" was analyzed from the peak of the CP subtracted from that of the control DNA (non IP with MBD) of the CP, while "CP-VZ" was analyzed from the peak of the CP subtracted from that of VZ. Biologically, "CP-cont" means the methylated region of differentiating neurons, while "CP-VZ" means the region methylated during neuronal differentiation.
|
| |
|
| Submission date |
Apr 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Itsuki Ajioka |
| Organization name |
Tokyo Medical and Dental University
|
| Department |
Center for Brain Integration Research
|
| Street address |
1-5-45 Yushima, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE37601 |
MBD-Seq of the V/SVZ and the CP at E16 |
| GSE37625 |
V/SVZ (ventricular/subventricular zone) tissue and CP (cortical plate) tissue at E16 |
|
| Relations |
| SRA |
SRX144780 |
| BioSample |
SAMN00990119 |
