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Sample GSM5373214 Query DataSets for GSM5373214
Status Public on Sep 23, 2021
Title RNA-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 1
Sample type SRA
 
Source name EBNA2+ (B95.8) EBV infected Ramos B cells
Organism Homo sapiens
Characteristics cell type: Ramos B cells
infection: EBNA+ (B95.8) Epstein-Barr virus (EBV)
Treatment protocol Cells were infected with EBV with EBNA+ strain (B95.8) and EBNA2- strain (P3HR1), respectively.
Growth protocol Cells were cultured in 10% FBS supplemented RPMI medium 1640 for 2 weeks.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the mirVANA Isolation Kit (Ambion) from Ramos B cells.
RNA was depleted of ribosomal RNA and sequenced at Cincinnati Children’s Hospital Medical Center (CCHMC) DNA Sequencing and Genotyping Core Facility.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNA_B95.8_rep1-rg11-E00017
Data processing Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using STAR (version 2.5.2a)(Dobin et. al., 2013).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
The featureCounts function (Rsubread version: 3.5.3) was used to count reads (Liao et al. 2014) and create non-normalized gene counts.
DESeq2 (version 3.5.3) was used to calculate differential gene expression (Love et al. 2014).
Genome_build: hg19; hg38
Supplementary_files_format_and_content: Non-normalized gene counts in a tab separated text file. Columns are 1) gene name; 2) non-normalized read count.
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: Differential genes identified by DESeq2 in a tab separated text file. Columns are 1) gene name; 2) log2FoldChange; 3) raw-pvalue; 4) adjusted p-value.
 
Submission date Jun 11, 2021
Last update date Oct 23, 2023
Contact name Matthew Weirauch
E-mail(s) Matthew.Weirauch@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Department Center for Autoimmune Genomics and Etiology (CAGE)
Street address 3333 Burnet Avenue
City Cincinnati
State/province Ohio
ZIP/Postal code 45229-3026
Country USA
 
Platform ID GPL11154
Series (2)
GSE148396 Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci
GSE177046 Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [RNA-seq]
Relations
BioSample SAMN19670367
SRA SRX11121544

Supplementary file Size Download File type/resource
GSM5373214_RNA_B95.8_rep1.gene_counts.hg19.tsv.gz 211.4 Kb (ftp)(http) TSV
GSM5373214_RNA_B95.8_rep1.gene_counts.hg38.tsv.gz 153.3 Kb (ftp)(http) TSV
GSM5373214_RNA_B95.8_rep1.hg19.bw 376.4 Mb (ftp)(http) BW
GSM5373214_RNA_B95.8_rep1.hg38.bw 411.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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