|
| Status |
Public on Feb 23, 2021 |
| Title |
11C |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CLL
patient id: 11
diagnosis: CLL
ighv: Unmutated
treatment status: pre-treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
bisulfite treated genomic DNA
RRBS
Sample excluded from analysis for quality control reasons. Processed data not available.
|
| Data processing |
Bulk RRBS processing: Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.05 -s 16 -w 100 -S 1 -R -u -m 0. Methylation rates were called using custom scripts and subsequently filtered for coverage (min 5).
Single cell processing: Adapter clipping and quality trimming using cutadapt. Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.1 -s 12 -q 20 -w 100 -S 1 -R -u -m 0. Methylation rates were called using mcall and subsequently filtered for coverage (min 10, max 250).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file from coverage filtered Bed file (<chr> <start> <end> <methylation rate>)
|
| |
|
| Submission date |
Jan 23, 2019 |
| Last update date |
Feb 23, 2021 |
| Contact name |
Helene Kretzmer |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Genome Regulation
|
| Lab |
Meissner Lab
|
| Street address |
Ihnestraße 63
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE125499 |
The altered DNA methylation landscape in chronic lymphocytic leukemia emerges early and persists after treatment |
|
| Relations |
| BioSample |
SAMN10792761 |
