|
| Status |
Public on Sep 23, 2021 |
| Title |
RNA-seq: uninfected Ramos B cells replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Uninfected Ramos B cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Ramos B cells
infection: None
|
| 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_uninfected_rep1-rg16-E00013
|
| 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 |
SAMN19670369 |
| SRA |
SRX11121542 |
