|
| Status |
Public on Nov 23, 2020 |
| Title |
PDAC1_Ep |
| Sample type |
SRA |
| |
|
| Source name |
EPCAM+/CD45- epithelial cells isolated from human PDAC sample
|
| Organism |
Homo sapiens |
| Characteristics |
material: Epithelial cells isolated by flow cytometry
tissue: PDAC
cell type: EPCAM+/CD45- epithelial cells
age: 61
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from sorted cells was isolated using the QIAamp DNA Micro Kit (Qiagen) according to the manufacturer’s instructions
Four tagmentation based sequencing libraries with different barcodes were generated per sample as previously described (Weichenhan et al. DNA Methylation Protoc. 2018)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The human reference genome (hg19) was in silico transformed for both the top strand (C to T) and bottom strand (G to A) using MethylCtools. Before alignment, trimming of adaptor sequences was performed using SeqPrep (https://github.com/jstjohn/SeqPrep). The first read in each read pair was then C to T converted and the second read in the pair was G to A converted. The converted reads were aligned to a combined reference of the transformed top strands (C to T) and bottom strands (G to A) using BWA (bwa-0.6.2-tpx) with default parameters but with disabling the quality threshold parameter for read trimming (-q) of 20 and the Smith-Waterman for the unmapped mate (-s).
After alignment, reads were converted back to the original states, and reads mapping to the antisense strand of the respective reference were removed. Duplicate reads were marked, and the complexity was determined using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Reads with alignment scores of less than 1 were filtered before subsequent analysis.
Only bases with Phred-scaled quality score of ≥ 20 were considered
The raw counts of methylated and unmethylated reads for each CpG site from different libraries were merged for each sample
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads per CpG is given as raw counts and as a ratio.
|
| |
|
| Submission date |
Nov 22, 2020 |
| Last update date |
Nov 23, 2020 |
| Contact name |
Elisa Espinet |
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE161956 |
Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin |
|
| Relations |
| BioSample |
SAMN16870647 |
