|
| Status |
Public on Dec 31, 2020 |
| Title |
Control_ncsMBC_1 |
| Sample type |
SRA |
| |
|
| Source name |
non-class-switched memory b cells
|
| Organism |
Homo sapiens |
| Characteristics |
source: fresh blood
cell type: non-class-switched memory b cells
diagnosis: healthy
molecule subtype: Bisulfite-treated genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp DNA micro kit (Qiagen) according to the manufacturer’s protocol
30 ng of genomic DNA was used to produce four independent barcoded sequencing libraries per DNA sample using the tagmentation method (Wang, Q. et al. Tagmentation-based whole-genome bisulfite sequencing. Nat. Protoc. (2013). doi:10.1038/nprot.2013.118)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
reads were trimmed using Trimmomatic
pre-processed and aligned using MethylCTools, with default parameters (V. Hovestadt, S. Picelli, B. Radlwimmer, M.Z. and P.L., unpublished data), which uses the Burrows-Wheeler alignment algorithm
methylation calling using methylCtools
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylaton callings for each Sample
|
| |
|
| Submission date |
Jul 22, 2019 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Esteban Ballestar |
| Organization name |
Josep Carreras Research Institute (IJC)
|
| Lab |
Epigenetics and Immune Disease
|
| Street address |
Ctra de Can Ruti, Camà de les Escoles s/n
|
| City |
Badalona, Barcelona |
| State/province |
N/A = Not Applicable |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE134664 |
The DNA methylomes of hyper-IgM syndrome type 2 B cells provide insights into the roles of activation-induced deaminase prior to the germinal center reaction |
| GSE172012 |
The DNA methylome and transcriptome of hyper-IgM syndrome type 2 B cells |
|
| Relations |
| BioSample |
SAMN12338009 |
| SRA |
SRX6487561 |
