|
| Status |
Public on Mar 05, 2021 |
| Title |
24hr_K3_Infected_Sorted_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA_HCMV infected K3 cells_24hpi
|
| Organisms |
Homo sapiens; Human betaherpesvirus 5 |
| Characteristics |
treatment: HCMV infected, 24 hr
rna type: total RNA
cell line: Kasumi-3
|
| Treatment protocol |
Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells.
|
| Growth protocol |
Kasumi-3 were grown in RPMI-1640 medium (ATCC 30-2001) supplemented with 20% fetal bovine serum (Corning) and 1,000 Units/ml Penicillin-Streptomycin (Gibco)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Infected Kasumi-3 cells were collected and lysed in Trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion step according to the manufacturer’s instructions.
RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: tab-delimited file with read counts per gene
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
Jan 14, 2021 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Mary Hummel |
| E-mail(s) |
m-hummel@northwestern.edu
|
| Phone |
847-322-6438
|
| Organization name |
Northwestern University
|
| Street address |
303 E. Chicago Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24958 |
| Series (2) |
| GSE164839 |
Transcriptome analysis of HCMV infected and mock-infected Kasumi-3 cells at 24 hours post infection |
| GSE164861 |
Epigenetic reprogramming of host and viral genes by Human Cytomegalovirus infection in Kasumi-3 myeloid progenitor cells at early times post-infection |
|
| Relations |
| BioSample |
SAMN17315728 |
| SRA |
SRX9849973 |
