|
| Status |
Public on Jan 17, 2018 |
| Title |
Ramos EBV pos |
| Sample type |
SRA |
| |
|
| Source name |
Ramos cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cKit+ splenocytes
infection: with EBV
|
| Treatment protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRUseq RNA sample kit (Illumina)
RNA was isolated from Ramos cell lines with and without EBV infection using the mirVANA Isolation Kit (Ambion). RNA sequencing targeting 150 million mappable 125 basepair reads from paired-end polyA enriched libraries was performed at the CCHMC DNA Sequencing and Genotyping Core Facility at CCHMC.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were aligned to the GrCh37 (hg19) build of the human genome using TopHat and Bowtie2 with Ensembl52 RNA transcript annotations as a guide. In parallel, these data were aligned to the EBV genome (NCBI).
For allelic analysis, sequencing reads were aligned to the GrCh37 (hg19) build of the human genome using Hisat2. Differential expression analysis was performed using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: EBV-Ramos.txt (TPM values)
|
| |
|
| Submission date |
Jan 17, 2017 |
| Last update date |
Dec 20, 2024 |
| 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 |
GPL16791 |
| Series (1) |
| GSE93709 |
Transcription factors operate across disease loci: EBNA2 in autoimmunity |
|
| Relations |
| BioSample |
SAMN06235142 |
| SRA |
SRX2497779 |
