|
| Status |
Public on Jun 01, 2012 |
| Title |
HCT116 5ng_Rep#2 |
| Sample type |
SRA |
| |
|
| Source name |
Colon cancer derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: HCT116 cell line
cell type: colon cancer
|
| Treatment protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Qiagen Puregene kit protocol; Library construction protocol: Genomic DNA was purified from cell lines and primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (2000U T4 DNA ligase per reaction). Fragments of 150-250 bp (reduced representation bisulfite sequencing) and 150-400 bp (for enhanced reduced representation bisulfite sequencing) were isolated after agarose gel electrophoresis and subjected to bisulfite conversion (single conversion round using Zymo Research EZ DNA Methylation Kit) and PCR amplification using paired-end Illumina primers (18 cycles). Libraries were sequenced using an Illumina Genome Analyzer II or HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Flowcell: FC63577AAXX
Lanes: 5, 6, 7, 8
|
| Data processing |
Reads were created by CASAVA 1.7 from the GA Iix and HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/). Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained. In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: hg18
|
| |
|
| Submission date |
Apr 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Altuna Akalin |
| E-mail(s) |
aakalin@gmail.com, ala2027@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
1305 york
|
| City |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE37454 |
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia |
|
| Relations |
| SRA |
SRX143587 |
| BioSample |
SAMN00862055 |
