|
| Status |
Public on Mar 05, 2021 |
| Title |
24hr_K3_Infected_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HCMV infected_24 hpi
|
| Organisms |
Homo sapiens; Human betaherpesvirus 5 |
| Characteristics |
treatment: HCMV infected, 24 hr
cell line: Kasumi-3
barcode: Ad2.7:CTCTCTAC
|
| 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 |
genomic DNA |
| Extraction protocol |
Cells were collected and resuspended in 50 μl of a transposase mix that included 25 μl of 2x Nextera Tagment DNA buffer (Illumina), 2.5 μl Nextera Tn5 transposase (Illumina), 0.5 μl digitonin 5% (Invitrogen), and 22μl of H2O. The reaction was carried at 37°C for 30 min. DNA was purified with Qiagen MinElute PCR purification kit and eluted in 10μl of buffer EB.
DNA libraries were amplified by using NEBNext High-Fidelity (New England Biolabs) and barcoded primers. The number of amplification cycles were calculated by qPCR and kept under 11 to prevent saturation. Libraries were purified with Qiagen MinElute PCR purification kit and sized selected with AMPure XB beads (Beckman Coulter) . Library quality control was assessed by Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and the libraries were sequenced with Illumina NextSeq technology (75bp single-end reads, 100 million reads/sample).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATACseq
|
| Data processing |
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
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: 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) |
| GSE164841 |
Chromatin accessibilty 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 |
SAMN17315789 |
| SRA |
SRX9849985 |
