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| Status |
Public on Jun 04, 2019 |
| Title |
XWGBS_GM12890 |
| Sample type |
SRA |
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| Source name |
GM12890
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12890
cell type: EBV-transformed lymphoblastoid cell line
number of cells: 2,000,000
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| Biomaterial provider |
Coriell; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12890
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| Treatment protocol |
None
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| Growth protocol |
Lymphoblatoid cell lines were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
2 million cells were pelleted at 2000g for 10' and frozen at -80C until extraction of DNA. Pellets were thawed and resspended in 10mM Tris pH 8.0, 150 mM EDTA solution before the addition of SDS to a final concentration of 1%. Protein was digested overnight at 50C with 25 ug of Proteinase K, followed by an hour incubation at 37C with 5 ug of RNAse A. Extraction of genomic DNA was then achieved through two consecutive phenol:chloroform steps, selecting the aqeous phase. The DNA was then concentrated and purified via ethanol precipitation.
100 ng of genomic DNA was treated with Tn5 transposase for tagmentation, then tagged DNA was filled with methylated dCTP, dATP, dGTP, dTTP mixture. The filled DNA was bisulphite treated using EZ DNA methylation Gold kit (Zymo research). The bisulphite treated samples were amplified with custom and Illumina index adapters. The amplified products were size selected using AMPureXP beads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
FASTQ reads were adapter asked using cutadapt v1.9.1 for bisulfite converted adapter sequences
Masked reads were aligned to hg38+decoy+EBV using bwa-meth v0.10 with default parameters
Aligned reads were marked for duplicates using Picard v2.4.1
A custom perl script was used to filter "fill-in" artifact be qc-fail flagging reads with 3 or more methylated CHH's outside the first 11 cycles
Methylation ratios were determined, by CpG, CHG, CHH context, using MethylDackel v0.1.13 with min baseQ >= 20, min mapQ >=20 and excluding the first 11bases of R1 and R2 alignments
Genome_build: GENCODE hg38 + decoy + EBV
Supplementary_files_format_and_content: Compressed methylKit files were generated which capture CpG CHG, CHH methylation and coverage (https://github.com/al2na/methylKit); meth_10_fil_no99.rds is a serliazed R object containing filtered CpG sites with >10 read depth
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| Submission date |
Jul 23, 2018 |
| Last update date |
Jun 04, 2019 |
| Contact name |
Andrew Johnston |
| E-mail(s) |
Andrew.Johnston@med.einstein.yu.edu
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| Organization name |
Albert Einstein College of Medicine
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| Department |
Genetics
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| Lab |
Price 314
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| Street address |
1301 Morris Park Avenue
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE117565 |
Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. [Bisulfite-Seq] |
| GSE117576 |
Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. |
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| Relations |
| BioSample |
SAMN09708688 |
| SRA |
SRX4452035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3303963_BS-TAG-Sample-90_CHG.methylKit.txt.gz |
1.5 Gb |
(ftp)(http) |
TXT |
| GSM3303963_BS-TAG-Sample-90_CHH.methylKit.txt.gz |
5.2 Gb |
(ftp)(http) |
TXT |
| GSM3303963_BS-TAG-Sample-90_CpG.methylKit.txt.gz |
414.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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