|
Status |
Public on Jun 04, 2019 |
Title |
ICAM1 hi LCL donor 2 |
Sample type |
SRA |
|
|
Source name |
ICAM1 high sorted EBV immortalized LCL
|
Organisms |
Homo sapiens; human gammaherpesvirus 4 |
Characteristics |
donor id: donor 2 source cell type: primary human B cells cell type: ICAM1 high 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 |
SAMN11947008 |
SRA |
SRX5961727 |