|
| Status |
Public on Oct 21, 2016 |
| Title |
1 dpi iNs -hMeDIP Sequencing |
| Sample type |
SRA |
| |
|
| Source name |
Induced neurons-1 dpi derived from Mouse embryoic fibroblats (MEFs)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MEF-derived induced neurons
passages: 3-5 passages
strain: ICR
|
| Growth protocol |
The primary mouse embryonic fibroblasts (MEFs) were routinely isolated from mouse embryos in fibroblasts medium. The primary neurons were obtained from the 1-day-old pups and cultured in neuronal medium. The induecd neurons were generated from fibroblasts and cultured in neuronal medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA were extrcted with the genomic DNA extraction Kit
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit (#FC-102-1002, Illumina)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
The sample was 1 dpi-iduced neurons and symboled hM002
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM002-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx / hM002 vs hM003(hypo); hM002 vs hM003(hyper)
|
| Data processing |
Library strategy: hMeDIP-Seq
Illumina Casava software used for basecalling.
The stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8)
Solexa CHASTITY quality filter were used to obtain the clean reads
The clean reads were aligned to mouse genome (UCSC MM10) using BOWTIE software (V2.1.0)
Aligned reads were used for peak calling of the hMeDIP regions using MACS V2.
Genome_build: mm10
Supplementary_files_format_and_content: FASTQ format files include the DNA methylation status of gene promoter and the gene body regions in all samples
|
| |
|
| Submission date |
Oct 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
J Z |
| E-mail(s) |
zhangjuanzh@126.com
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
State Key Laboratory of Stem Cell and Reproductive Biology
|
| Lab |
Group of Neural Stem Cell and Neurogenesis
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE88867 |
The DNA modification is dynamic during the conversion from fibroblasts to neurons [Hydroxymethylation] |
| GSE88869 |
The DNA modification is dynamic during the conversion from fibroblasts to neurons |
|
| Relations |
| BioSample |
SAMN05916102 |
| SRA |
SRX2251203 |
