|
| Status |
Public on Jul 19, 2022 |
| Title |
260_WGBS |
| Sample type |
SRA |
| |
|
| Source name |
Primary AML
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Selected PBMC or BM cells
assay: WGBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA bisulfite treatment was performed using the EZ DNA Methylation-Gold Kit (catalog D5005, Zymo Research Corporation) according to the manufacturer's instructions. The recovered bisulfite-converted single-stranded DNA was processed for library construction using the Accel-NGS@Methyl-seq DNA Library kit (catalog 30024, Swift BioSciences) as per manufacturer instructions.
Briefly, using the Adaptase module, truncated adapter sequences were incorporated to the single-stranded DNA in a template-independent reaction through sequential steps. DNA was then enriched using 6 cycles of PCR with primers compatible with Illumina sequencing. The quantity and molecular size of the library was confirmed by Qubit HS DNA assay (ThermoFisher) and Tapestation 2200 system coupled with High Sensitivity D1000 ScreenTapes (Agilent). Illumina 8-nt dual-indices were used for multiplexing. Samples were pooled and sequenced on Illumina NovaSeq S4 sequencer for 150 bp read length in paired-end mode, with an output of 580 million reads per sample.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were first trimmed using Trim_Galore! (version 0.6.0) with “--paired --clip_R1 10 --clip_R2 10” options
Trimmed reads were then mapped with “bismark” command and deduplicated using Bismark’s “deduplicate_bismark” tool with default parameters
Per-cytosine methylation level was obtained using methylpy (version 1.4.2) “call-methylation-state” tool with “--binom-test True --paired-end True” options
CG methylation levels bigwig files were generated with methlypy (version 1.4.2) with "methylpy allc-to-bigwig --bin-size 10"
genome build: hg38
processed data files format and content: Bigwig, CG methylation levels at 10bp bins
|
| |
|
| Submission date |
Jun 09, 2020 |
| Last update date |
Jul 19, 2022 |
| Contact name |
Feng Yue |
| Organization name |
Northwestern University
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
303 E Chicago Ave. Simpson Querrey 7-518
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE152099 |
Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia [WGBS] |
| GSE152136 |
Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia |
|
| Relations |
| BioSample |
SAMN15192086 |
