|
| Status |
Public on Oct 31, 2018 |
| Title |
RRBS_control_3_p8 |
| Sample type |
SRA |
| |
|
| Source name |
Human dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Dermal fibroblasts
genotype: wild type
passage: 8
|
| Growth protocol |
Cells were cultured in DMEM, 10% FBS, 1% pen/strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from human fibroblast was extracted using QIAamp DNA mini kit according to the manufacturer's instructions
500ng/sample of extracted DNA was digested with Msp1 enzyme (NEB #R0106M) Methylated adaptors (NEB #E7535L) were ligated with T4 ligase (NEB #M0202M) following by qPCR amplification with Illumina indexing primers. Libraries clean up and size selection was done using Agencourt® AMPure® XP magnetic beads (Beckman Coulter # A63881).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Bsmap was used for initial data processing, methylation calls ans reads alignment.
Methylkit was used to do analysis and statistic of differentially methylated regions, specific parameters: 100 bp step-wise tiling windows, 1 CpG minimum per tile and a minimum 20x CpG coverage of each tile per sample.
Significant DNA methylation changes ≥ 30%.
HOMER was used for sequences annotations.
HOMER was used to analyze DNA binding motifs
Genome_build: hg19
Supplementary_files_format_and_content: .map : file containing raw methylation calls. There is one file per sample.
|
| |
|
| Submission date |
Feb 14, 2018 |
| Last update date |
Nov 01, 2018 |
| Contact name |
Gregor Ulrich Andelfinger |
| E-mail(s) |
gregor.andelfinger@recherche-ste-justine.qc.ca
|
| Phone |
514 345 4931 5401
|
| Organization name |
CHU Sainte-Justine
|
| Department |
Cardiology
|
| Street address |
3175, Chemin de la Côte-Sainte-Catherine
|
| City |
Montréal |
| State/province |
QC |
| ZIP/Postal code |
H3T 1C5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE110601 |
Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. [BiSulfite-seq] |
| GSE110612 |
Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. |
|
| Relations |
| BioSample |
SAMN08536411 |
| SRA |
SRX3699578 |
