|
| Status |
Public on Jun 04, 2019 |
| Title |
ICAM1 lo LCL donor 1 |
| Sample type |
SRA |
| |
|
| Source name |
ICAM1 low sorted EBV immortalized LCL
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
donor id: donor 1
source cell type: primary human B cells
cell type: ICAM1 low LCL latency III
ebv strain: EBV B95-8
|
| Growth protocol |
All latency III LCLs were grown in complete RPMI + 10% FBS + Pennicillin/Streptomycin/Glutamine in 5%CO2. Latency IIb cells were grown in complete RPMI + 15% FBS + Pennicillin/Streptomycin/Glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using a Qiagen Rneasy Kit
mRNA sequencing libraries were prepared using the Kappa Stranded RNA-seq Library Preparation Kit accoridng to the manufacturers instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastq files were aligned to the human genome (hg38) using hisat2
BAM files were converted to SAM files
Stringtie was used to assemble transcripts
Assembled transcripts were imported into the R package ballgown
Ballgown was used to determine differential gene expression and calculate RPKM
Genome_build: hg38
Supplementary_files_format_and_content: processed data contains gene level RPKMs, transcript level RPKMs and genomic locations as well as differential gene expression fold changes, pvalues and FDR q values
|
| |
|
| Submission date |
Jun 03, 2019 |
| Last update date |
Jun 05, 2019 |
| Contact name |
Micah Alan Luftig |
| E-mail(s) |
micah.luftig@duke.edu
|
| Organization name |
Duke University
|
| Department |
Molecular Genetics and Microbiology
|
| Lab |
Luftig Laboratory
|
| Street address |
213 Research Drive CARL Building Room 0045
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL23362 |
| Series (1) |
| GSE132138 |
Identification of Host Biomarkers of EBV Latency IIb and Latency III |
|
| Relations |
| BioSample |
SAMN11947014 |
| SRA |
SRX5961721 |
