|
| Status |
Public on Dec 16, 2015 |
| Title |
RNA-seq in LCL, EBNA1 shRNA, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
LCL_EBNA1 shRNA_RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LCL
cell type: EBV positive B-cell
transduced with: shEBNA1 lentivirus
|
| Treatment protocol |
LCL cells transduced with either pLKO.1 shControl or shEBNA1 lentivirus after 5 days of puromycin selection
Cells were maintained and isolated in logarihmic growth phase for ChIP-assays. RNA Seq analysis was performed with LCL cells transduced with either pLKO.1 shControl or shEBNA1 lentivirus after 5 days of puromycin selection.
|
| Growth protocol |
EBV positive B-cell (Raji, Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax. EBV positive NPC-line C666-1 was grown in DMEM with 10% FBS and Glutamax.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA isolated using Trizol reagent
TruSeq Stranded Total RNA Library Preparation kit
ChIP-Seq protocol is as described previously (Lu et al, 2010 Virology journal 7, 262). Total RNA was isolated for RNA-Seq using Trizol reagent.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA.LCL.shEBNA1.1
|
| Data processing |
All chip-seq files were generated by Illumina GA II and base calling was done with CASAVA 1.5
Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software with -center -o, -fdr 0.2
RNA-Seq data analyzing was done with rsem(ver. 1.2.3) and Hg19 genome with UCSC known gene set.
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output while expression file contains the edgeR output; details in the 'readme.txt'
|
| |
|
| Submission date |
Oct 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
[email protected]
|
| 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 |
GPL16791 |
| Series (1) |
| GSE73887 |
Identification of MEF2B, EBF1, and IL6R as chromosome bound targets of EBNA1 essential for EBV infected B-lymphocyte survival |
|
| Relations |
| BioSample |
SAMN04158416 |
| SRA |
SRX1322307 |
