|
| Status |
Public on Oct 25, 2023 |
| Title |
Mock_N_hmC_2 |
| Sample type |
SRA |
| |
|
| Source name |
NeuN Negative
|
| Organism |
Mus musculus |
| Characteristics |
treatment: mock
cell type: NeuN Negative
|
| Treatment protocol |
Maternal mouse were treated by ZIKA virus or PBS as Mock control
|
| Growth protocol |
NeuN positive and NeuN negative cells were isolated from P30 mouse cortex
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by adding equal volume of buffered phenol:chloroform:isoamyl alcohol (25:24:1 ratio) and centrifuged in Phase-Lock tubes at 15,000 RPM at room temperature. Supernatant was transferred to clean tubes. An equal volume of isopropanol was then added to the supernatant and mixed well at room temperature to precipitate the DNA. The DNA was then centrifuged at 10,000g for 10 minutes at room temperature, and then washed in 70% ethanol. After all ethanol was removed, the DNA pellet was eluted in nuclease-free water and incubated at 55 for 1 hour before storing at -20.
5mg of genomic DNA was sonicated to 300-400 base pairs and 5hmC containing fragments were glucosylated (T4 phage ß-glucosyltransferase enzyme and UDP-6-N3-glucose). The glucosylated fragments were purified and then biotinylated (disulfide biotin linker) and pulled down with Dynabeads MyOne Streptavidin C1 beads. The 5hmC fragments were released from the beads using dithiothreitol and purified for a final time. DNA fragments were eluted in nuclease-free water and quantified by Qubit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired end sequencing reads of MeDIP-seq library and 5hmC-Seal-seq library were firstly mapped to human genome (hg38) by Bowtie 2 (2.4.4) (2) with “--no-mixed --no-discordant”.
Aligned reads in bam file were sorted by genomic coordinate by samtools.
Peaks for were identified by MACS2 version 2.2.6 with their corresponding input bam file
Assembly: mm9
Supplementary files format and content: narrowPeak
Library strategy: 5hmC-Seal-seq
|
| |
|
| Submission date |
Aug 08, 2023 |
| Last update date |
Oct 25, 2023 |
| Contact name |
Bing Yao |
| E-mail(s) |
bing.yao@emory.edu
|
| Phone |
3523596473
|
| Organization name |
Emory University
|
| Department |
Department of Human Genetics
|
| Street address |
615 Michael Street
|
| City |
Atlanta |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE240415 |
Brain methylome remodeling sustains neuronal activity gene expression in mice exposed to maternal immune activation [5hmc] |
| GSE240417 |
Brain methylome remodeling sustains neuronal activity gene expression in mice exposed to maternal immune activation |
|
| Relations |
| BioSample |
SAMN36893441 |
| SRA |
SRX21302198 |
