|
| Status |
Public on Jul 16, 2019 |
| Title |
Input_AM_DNA |
| Sample type |
SRA |
| |
|
| Source name |
dorsal cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: dorsal cortex
age: E14.5
genotype: WT
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei of E14.5 dorsal cortex and Ash2l/histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The 75-nt sequence reads generated by Illumina sequencing were mapped to the genome using the Burrows-Wheeler Aligner algorithm with default settings.Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the mouse genome (mm10) were used in the subsequent analysis
For identifying intervals over input control, the MACS cutoff for the false discovery rate after controlling for significance was P=1×10^ –7.
The two main peak callers used at this study are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig. Files with extension *.bw. Binary files that can be opened in or uploaded to genome browsers and show the fragment density for 32-nt bins along the genome (“signal map”)
|
| |
|
| Submission date |
Oct 09, 2018 |
| Last update date |
Jul 17, 2019 |
| Contact name |
Xiaozhong Peng |
| E-mail(s) |
pengxiaozhong@pumc.edu.cn
|
| Phone |
86 69156434
|
| Organization name |
Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College
|
| Department |
Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences
|
| Lab |
Lab of Xiaozhong Peng
|
| Street address |
No.5, Dongdan Santiao, Dongcheng District
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE120987 |
COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling [ChIP-seq] |
| GSE120988 |
COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling |
|
| Relations |
| BioSample |
SAMN10221671 |
| SRA |
SRX4816222 |
