|
Status |
Public on Mar 11, 2022 |
Title |
Lamin AC WT cells under untreated condition, replicate 2 |
Sample type |
SRA |
|
|
Source name |
GM12878 cell line
|
Organisms |
Homo sapiens; human gammaherpesvirus 4 |
Characteristics |
lamins: WT treatment: unt replicate: 2
|
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 WT cells under untreated condition, replicate 2
|
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 |
SAMN20456351 |
SRA |
SRX11582948 |