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Sample GSM3847126 Query DataSets for GSM3847126
Status Public on Jun 04, 2019
Title ICAM1 lo LCL donor 2
Sample type SRA
Source name ICAM1 low 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 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
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
BioSample SAMN11947010
SRA SRX5961725

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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