|
| Status |
Public on Dec 17, 2018 |
| Title |
5570_BA9_neg (bisulfite-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
NeuN negative nuclei sorted from prefrontal cortex (BA9)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NeuN neg
tissue: prefrontal cortex (BA9)
individual id: 5570
|
| Treatment protocol |
DNA was extracted from intact brain tissues or neuronal and non-neuronal nuclei isolated from brain tissues (for samples with "_pos" or "_neg" at end of sample ID) and sorted via FACS based on NeuN staining as in Montano et al. 2013.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Epicentre MasterPure DNA Purification Kit (cat#: MCD85201)
NEBNext Ultra DNA library Prep kit for Illumina followed by size selection (300-400bp), bisulfite conversion with EZ DNA Methylation-Gold kit (cat#:D5005,Zymo), and amplification using Kapa hifi Uracil+ (cat#:KK282, Kapa Biosystems).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
WGBS raw sequencing reads were trimmed using Trim Galore! (v0.4.0) and aligned using Bismark (v0.14.3) against human genome version hg19/GRCh37. Bismark's bismark_methylation_extractor was used to call CpG methylation and the output was read into bsseq (v1.10.0) for analysis using the BSmooth method (Hansen et al 2012).
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: The "M" and "Cov" matrices for all sorted and intact tissue samples are provided as text files. "M" matrix contains the number of reads supporting methylation at each CpG for each sample while the "Cov" matrix contains the number of reads covering each CpG for each sample.
|
| |
|
| Submission date |
Mar 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew P. Feinberg |
| Organization name |
Johns Hopkins University School of Medicine
|
| Street address |
855 N. Wolfe St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE96612 |
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [Bisulfite-Seq] |
| GSE96615 |
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability |
|
| Relations |
| BioSample |
SAMN06603234 |
| SRA |
SRX2640487 |
