|
| Status |
Public on Mar 05, 2021 |
| Title |
GFPGR3 |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SH-SY5Y
genotype: GFP
differentiation phase: Growth
cell line replicate: 3
|
| Treatment protocol |
Cells were transfected with piggyBac plasmids via Lipofectamine 3000
|
| Growth protocol |
Cells were grown and differentiated according the protocol from Shipley et al. (PMID: 26967710)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from flash frozen cell pellets using the QIAamp DNA Micro kit (Qiagen)
Accel-NGS Methyl-Seq DNA Library Kit
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Mar 07, 2021 |
| Contact name |
Benjamin I Laufer |
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE168276 |
Stable DNMT3L Overexpression in SH-SY5Y Neurons Recreates a Facet of the Genome-Wide Down Syndrome DNA Methylation Signature |
|
| Relations |
| BioSample |
SAMN18142603 |
| SRA |
SRX10240618 |
