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| Status |
Public on Sep 17, 2013 |
| Title |
EBV transformed B-cells from Individual B2 |
| Sample type |
SRA |
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| Source name |
EBV transformed B-cells
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| Organism |
Homo sapiens |
| Characteristics |
individual/donor id: B2
sample group: EBV transformation into LCL
time point: week6 following EBV infection
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| Treatment protocol |
Cells were either resting, CD40 activated or EBV transformed
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Epicentre Masterpure DNA isolation kit
Bisulfite converted Illumina TruSeq DNA library
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
B2_transformed
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| Data processing |
Basecalls performed using CASAVA 1.8.1
Reads were aligned to bisulfite-treated genome with the Bsmooth pipeline, version 0.4.5-beta, with --bscpg option
The Bsmooth alignment pipeline used Bowtie 2.0.0-beta8 with --ignore-quals option
Only summarized data with a quality score greater than 20 was used. Data was processed using the Bsmooth function from the bsseq package from Bioconductor. Each sample was processed twice, one for small scale smoothing (used to find small DMRs, parameters were h = 1000, ns = 70) and once for large scale smoothing (used to find large hypomethylated blocks, parameters were h=20000,ns=500)
Only CpGs which had at least 2 samples with a coverage of 2 or more in each of the following 3 group (B1,B2,B3 activation), (B1,B2,B3 resting) and (B1,B2,B3 transformed)
Genome_build: human NCBI genome build 37, lambda phage (gi|9626243|ref|NC_001416.1|) and EBV virus (gi|86261677|emb|AJ507799.2|)
Supplementary_files_format_and_content: Rows are CpGs, columns are as follows: chr (chromosome) and pos (position) is genomic location. Cov is the number of reads covering the CpG and M is the number of reads covering the CpGs, supporting methylation. smallSmooth and largeSmooth are smoothed values for small and large scale smoothing.
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| Submission date |
Aug 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kasper Daniel Hansen |
| E-mail(s) |
kasperdanielhansen@gmail.com
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| Phone |
5103335965
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| Organization name |
Johns Hopkins
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| Department |
Biostatistics
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| Lab |
Hansen
|
| Street address |
615 N Wolfe St. E3527
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE49627 |
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization [Bisulfite-seq] |
| GSE49629 |
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization |
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| Relations |
| BioSample |
SAMN02304080 |
| SRA |
SRX332383 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1202811_B2_transformed.csv.gz |
408.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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