|
| Status |
Public on Jul 01, 2014 |
| Title |
Treated AZA BS-seq Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
AML3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AML3
treatment: Aza
|
| Treatment protocol |
AzaC was dissolved from lyophilised powder into culture-sterile DMSO to produce a 20 mM stock solution and stored as 15μl aliquots at -80°C. For each new experiment a fresh aliquot of AzaC was diluted in RPMI/20% FBS to produce a 2 mM working stock which was diluted directly onto cells in culture.
|
| Growth protocol |
OCI-AML3 cells were cultured in suspension in RPMI media supplemented with FBS 20%, Penicllin 5% and L-Glutamine 5%, incubated at 37°C in humidified conditions and 5% CO2. To passage, cells were counted by haemocytometer and either centrifuged to a pellet and resuspended in fresh media or resuspended in 50% fresh media at a concentration of 0.5 x 106/ml every 2-3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with phenol-chloroform method.
Libraries were prepared by BGI, Shenzhen. Briefly, DNA is fragmented and methylated adapters are ligated to DNA fragments. DNA is bisulphite treated and sequenced on Illumina platforms as per manufacturers instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bisulphite sequencing of AZA treated cells
|
| Data processing |
Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to hg18 whole genome using bismark v0.5.1 (bowtie v0.12.7) with directional setting and chunkmbs set to 256. Remaining default settings.
Multiple reads where both ends of the fragment align to the same genomic positions on the same strand were reduced to a single instance. Reads with more than 3 methylated cytosines in non-CpG contexts are discarded.
Reads are summarised on a per-CpG basis.
Genome_build: hg18
Supplementary_files_format_and_content: Summary files represent the number of reads supporting methylated/unmethylated bases at each CpG sequenced in that sample (Format is: chr <tab> position <tab> methylated reads <tab> unmethylated reads). bigWig files represent the percentage methylation at a given CpG (filtered to exclude CpGs with low coverage on a per replicate basis – >=10 reads in at least one sample & >=3 read in the other) and generated using UCSC wigToBigWig.
|
| |
|
| Submission date |
Feb 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Adams |
| Organization name |
University of Glasgow, Beatson Institute for Cancer Research
|
| Street address |
Switchback Rd, Bearsden
|
| City |
Glasgow |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE55124 |
Genome-wide methylation maps for untreated and Aza treated AML3 cells |
| GSE55125 |
Aza treated AML3 cells |
|
| Relations |
| BioSample |
SAMN02645187 |
| SRA |
SRX472622 |
| Named Annotation |
GSM1329865_CpG_context_AML1.percent.bigWig |
