|
| Status |
Public on Aug 13, 2020 |
| Title |
Day 3 sgAAVS1 Rep. 1 |
| Sample type |
SRA |
| |
|
| Source name |
BC-3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: BC-3 Cas9 cells
genotype: WT
|
| Treatment protocol |
Cas9 or dCas9-KRAB cells were infected with lentiviruses expressing sgRNAs against AAVS1, IRF4, BATF, MDM4 or vIRF3.
|
| Growth protocol |
All cells were grown in RPMI-1640 containing 10 µg/mL gentamycin, 0.05 mM β-mercaptoethanol and 20% Serum Plus-II media. Cells were maintained at densities between 2E5 and 1E6 cells/mL
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Harvested cell pellets were resuspended in 1 mL TRIzol reagent and purified using Direct-zol RNA Miniprep with in-column DNAseI digestion. Total RNA was eluted in 50 µL water.
mRNA-Seq libraries were constructed by the University of Chicago Genomics Facility using the TruSeq RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
mRNA-Seq reads were aligned to hg19 and KSHV genomes using STAR-Seq. Raw read counts were generated using HTSeq. Differential gene expression analysis was performed using DESeq2 (KO/KD vs. respective AAVS1 control)
Genome_build: hg19, KSHV (BAC16 reference)
Supplementary_files_format_and_content: FPKM or HTSeq counts
|
| |
|
| Submission date |
Jun 13, 2019 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Eva Gottwein |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University
|
| Department |
Microbiology-Immunology
|
| Street address |
320 E Superior St., Tarry building, Room 6-752
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE132707 |
mRNA-Seq of BC-3 IRF4 KO, BATF KO, and vIRF3 KD |
|
| Relations |
| BioSample |
SAMN12052128 |
| SRA |
SRX6066706 |
