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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 17, 2017 |
| Title |
WM373 cell line (metastatic cell line) |
| Sample type |
SRA |
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| Source name |
metastatic melanoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: WM373
cell type: metastatic melanoma cell line
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown under standard conditions (5% CO2, 37°C, humidified atmosphere). : DNA from the cell pellets were extracted using Pure link Genomic DNA mini kit (Invitrogen, Hilden, Germany) following the manufacturer’s protocol, with the modification of proteinase K treatment being performed overnight at 55°C.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 49bp run.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
DNA from 7 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment was done using Bismark program.
UNIX scripts and our in house developed tool DMAP (Chatterjee et al 2012, Nucleic Acids Research) was used for post processing of the data
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt files describing methylation status of each filtered CpG sites.
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| Submission date |
Jul 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Aniruddha Chatterjee |
| E-mail(s) |
aniruddha.chatterjee@otago.ac.nz
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| Phone |
+64-210701558
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| Organization name |
University of Otago
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| Department |
Pathology
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| Lab |
Epigenetics and Disease
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| Street address |
270 Great king Street
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| City |
Dunedin |
| State/province |
Otago |
| ZIP/Postal code |
9054 |
| Country |
New Zealand |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE70621 |
Analysis of paired primary and metastatic cell lines identifies common DNA methylation changes in melanoma metastasis. |
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| Relations |
| BioSample |
SAMN03846916 |
| SRA |
SRX1085031 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1812010_WM373_bismark.pcmethgenloc.txt.gz |
9.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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