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Sample GSM923104 Query DataSets for GSM923104
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

Supplementary file Size Download File type/resource
GSM923104_02_CP-VZ_annot.xls.gz 2.0 Mb (ftp)(http) XLS
GSM923104_02_CP-cont_annot.xls.gz 5.0 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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