|
| Status |
Public on Mar 05, 2021 |
| Title |
Nascent_RNA_Infected_K3_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Nascent RNA Infected K3
|
| Organisms |
Homo sapiens; Human betaherpesvirus 5 |
| Characteristics |
treatment: HCMV infected, 24 hr, EU-labeled, biotinylated RNA purified
rna type: nascent RNA
cell line: Kasumi-3
|
| Treatment protocol |
At 24 hr post-infection, HCMV infected cells were sorted for GFP expression and live cells while mock-infected cells were sorted for live cells. Newly synthesized RNA was labeled for 4 hr with 5-ethynyl uridine. A portion of the RNA was saved for analysis of steady state RNA, and the nascent RNA was purified by biotinylation of EU-labeled RNA and selection on Streptavidin beads. cDNA was prepared from each of the four RNA populations and the cDNA was purified with a Qiagen minElute PCR purification kit.
|
| 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 |
The cDNA was quantitated by qubit and processed into NGS libraries using the Swift BioSciences ACCEL-NGS® 1S PLUS DNA LIBRARY KIT in combination with the Swift BioSciences 1S Unique Dual Indexing Kit. Library QC (quality and quantity) was done by Bio-analyzer and the pool of libraries was sequenced on the Illumina NextSeq using Illumina reagents and protocols
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| 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) |
| GSE164843 |
Comparison of HCMV nascent and steady state transcriptomes expresssed in the Kasumi-3 latency model at early times 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 |
SAMN17315689 |
| SRA |
SRX9850009 |
