|
| Status |
Public on Apr 08, 2014 |
| Title |
T2N RRBS |
| Sample type |
SRA |
| |
|
| Source name |
twin 2_euploid_fetal primary fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Eupoid
tissue: Fetal primary fibroblasts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit.
RRBS protocol: genomic DNA digested with MspI restriction enzyme, end repair, A-tailing,adapter ligation, size selection, bisulfite conversion, PCR amplification
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling performed with CASAVA version 1.7
Mapping using Bismark aligner (-n 3 -l 20 -I 20)
MethylKit R package was used to calculate methylation percentages per each CpG
Genome_build: hg19
Supplementary_files_format_and_content: methT21_N.txt: genomic position of each CpG, methylation percentage in T1DS, methylation percentage in T2N
|
| |
|
| Submission date |
Mar 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Audrey Letourneau |
| E-mail(s) |
audrey.letourneau@unige.ch
|
| Organization name |
University of Geneva Medical School
|
| Department |
Genetic Medicine and Development
|
| Street address |
Rue Michel-Servet 1
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE55426 |
Domains of genomewide gene expression dysregulation in Down syndrome |
| GSE55505 |
Domains of genomewide gene expression dysregulation in Down syndrome [RRBS] |
|
| Relations |
| BioSample |
SAMN02671053 |
| SRA |
SRX480681 |
