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| Status |
Public on Dec 21, 2023 |
| Title |
SMS2.WGS |
| Sample type |
SRA |
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| Source name |
derived from human PBMC
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| Organism |
human gammaherpesvirus 4 |
| Characteristics |
host disease: MS
cell line: spontaneous lymphoblastoid cell lines
cell type: B cell
genotype: EBV
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from SLCLs using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). The Illumina DNA preparation kit was used for sequencing library preparation according to the manufacturer’s instructions. Sequencing was done with an Illumina NextSeq 500 system in high-output mode to generate a total of ∼4 × 108 paired-end 75-bp reads.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
MS_WGS_consensus.txt
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| Data processing |
Fastq reads were aligned against the EBV genome (accession NC_007605.1) using the BWA algorithm. Analysis of heterogeneous sites was performed following the procedure described by Čejková et al.. The consensus EBV genome for each sample was extracted using samtools59. Circus plots were generated using the R BioCircos package. Proteins were translated from nucleotide sequences using Geneious prime 2022.2 (https://www.geneious.com). Nucleotide and protein sequences were aligned using MAFFT v7.407 and visualized using Geneious prime 2022.2. Reference EBNA1 regions, in addition to the sequence from NC_007605.1, were obtained by querying each SLCL-derived sequence against nr using tblastn and taking differentially occurring sequences between matches for the three groups of samples (HC, AMS, SMS). One representative for each of three groups of identical sequences was kept. A phylogenetic tree of the 13 resulting sequences (9 samples, 4 reference) was constructed using PhyML with default parameters and visualized using iTOL.
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| Submission date |
Dec 22, 2022 |
| Last update date |
Mar 22, 2024 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
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| Phone |
2154956837
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| Organization name |
The Wistar Institute
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| Department |
Bioinformatics
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| Lab |
Genomics
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL34327 |
| Series (2) |
| GSE221624 |
Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells [EBV WGS] |
| GSE221625 |
Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells |
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| Relations |
| BioSample |
SAMN32376249 |
| SRA |
SRX18832362 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6891925_SMS2.WGS.bw |
604.8 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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