|
| Status |
Public on Feb 14, 2014 |
| Title |
Ad_Front.MethylC-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Adult brain prefrontal cortex tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain prefrontal cortex
developmental stage: Adult (42-year-old)
Sex: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen Blood & Cell Culture DNA Kits following the manufacture’s instructions
The DNA sample for MethylC-Seq was the same batch of sheared genomic DNAs with spike-in controls for TAB-Seq without the glucosylation and oxidation preparation. Both DNA samples for TAB-Seq and MethylC-Seq (0.5 ~ 1 μg) were end repaired, A-tailed, and ligated to methylated adaptors using Illumina TruSeq Sample Preparation Kits following the manufacturer’s instructions. Then ligated fragments were bisulfite converted using the the MethylCode kit (Invitrogen). Bisulfite-treated DNA was separated into three reactions for PCR-amplification using PfuTurbo Cx Hotstart DNA polymerase (Agilent Technologies) for 7 cycles, yielding three independent libraries for the same biological sample. Final libraries were purified with 1× AMPure XP beads then sequenced using Illumina Hiseq 2000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MethylC-seq
|
| Data processing |
Base calling is performed by CASAVA_v1.8.2
Alignment is performed by Bismark v0.7.6
Convert alignment results to information of each base of reference sequence, using SAMTools mpileup v0.1.18 (r982:295)
Calculate modification p-value of each site using R (version 2.14.2) function dbinom(), then assess FDR using Benjamini-Hochberg method
Genome_build: hg19
Supplementary_files_format_and_content: mC/hmC modification level of each site
|
| |
|
| Submission date |
May 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuexi Tan |
| E-mail(s) |
tanyuexi@gmail.com
|
| Organization name |
Tsinghua University
|
| Street address |
1 Qinghua Yuan, Haidian Dist.
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46710 |
Whole-genome analysis of 5-hydroxymethylcytosines and 5-methylcytosines at base resolution in human brain |
|
| Relations |
| Reanalyzed by |
GSE77019 |
| BioSample |
SAMN02141269 |
| SRA |
SRX275878 |
