|
| Status |
Public on Mar 11, 2022 |
| Title |
Lamin AC KO cells under untreated condition, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878 cell line
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
lamins: KO
treatment: unt
replicate: 1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Trizol (Invitrogen) for all RNA preparations, then subsequently cleaned and DNase treated using RNeasy columns (Qiagen)
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Lamin AC KO cells under untreated condition, replicate 1
|
| Data processing |
RNA-Seq data analysis was done with bowtie2 and rsem (ver. 1.2.3) using EBV genome version NC_007605.1
DESeq2 was used for differentail expression analysis
Genome_build: NC_007605.1
Supplementary_files_format_and_content: Prosessed files contains the raw counts for EBV genes
|
| |
|
| Submission date |
Jul 28, 2021 |
| Last update date |
Mar 11, 2022 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30446 |
| Series (2) |
| GSE181012 |
Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression [RNA-seq] |
| GSE198413 |
Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression |
|
| Relations |
| BioSample |
SAMN20456354 |
| SRA |
SRX11582953 |
