|
| Status |
Public on Jun 25, 2019 |
| Title |
3545_WGBS_Olig2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain BA46
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
brain region: Brodmann Area 46 (BA46)
cell type: Olig2
subject id: 3545
age: 80
disease state: Control
Sex: M
|
| Treatment protocol |
Human post-mortem brain tissue from the Brodmann Area 46 (BA46) was obtained. NeuN+ and OLIG2+ nuclei were purified employing fluorescence activated nuclei sorting (FANS)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from 1mg to 5mg of tissue sample, using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to manufacturer’s instructions. The extracted DNA was suspended in TE buffer and quantified by Qubit (Thermo Fisher Scientific).
Libraries were made with In-House Illumina sequencer compatible protocol. The extracted DNA was fragmented by S-series focused ultrasonicator (Covaris) using the “200bp-target peak size protocol”. Fragmented DNA was then size selected (200bp-600bp) with Agencourt aMPure XP bead-based (Beckman Coulter Cat. No. A63880) size selection protocol (Mark. A. Urich et al. 2015). The DNA End repair step was performed with End-It DNA end repair kit (Epicentre, Cat. No. ER81050. After End repair step, A-tailing (NEB, cat. No. M0202) and Ligation steps are performed to ligate methylated adaptors. Bisulfite treatment of genomic DNA was performed using the MethylCode Bisulfite Conversion Kit (Life technologies). Purified genomic DNA was treated with CT conversion reagent in a thermocycler for 10 minutes at 980C, followed by 2.5 hours at 640C. Bisulfite-treated DNA fragments remain Single-stranded as they are no longer complementary. Low-cycle (4-8) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (KAPA Biosystems, cat. No. KK2801) which can tolerate Uracil residues. The final library fragments contain Thymines and Cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Quality and adapter trimming was performed using TrimGalore version 0.4.1 (Babraham Institute).
Reads were mapped to the human GRCh37 reference genome using Bismark version: v0.14.4 (Krueger and Andrews 2011) and Bowtie
Methylation calling was performed after deduplication using Bismark
Bsseq bioconductor package and Bsmooth (Hansen et al 2012) were used to process CpG methylation data
Genome_build: GRCh37
Supplementary_files_format_and_content: Methylated read count and coverage for CpGs
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
Nov 14, 2019 |
| Contact name |
Soojin V Yi |
| E-mail(s) |
soojinyi@gatech.edu
|
| Organization name |
Georgia Institute of Technology
|
| Department |
School of Biology
|
| Street address |
950 Atlantic Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30318 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE107729 |
Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS] |
| GSE108066 |
Contribution of differential cell-specific methylation to schizophrenia |
|
| Relations |
| SRA |
SRX3468761 |
| BioSample |
SAMN13282190 |
