|
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)
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|
|
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.
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|
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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 |