|
| Status |
Public on Nov 19, 2022 |
| Title |
Rep3 t24 siPNUTS |
| Sample type |
SRA |
| |
|
| Source name |
iSLK-BAC16 (WT)
|
| Organisms |
Homo sapiens; Human gammaherpesvirus 8 |
| Characteristics |
cell type: iSLK cells
virus: BAC16 infectious clone
treatment: siPNUTS
induction: 1mM Sodium butyrate + 1 ug/mL doxycycline (24hr)
|
| Treatment protocol |
Cells at 60-80% confluency were treated with 30 nM siRNA. Twenty-four hours later, cells were split and 24 hrs after that (48 hrs post-siRNA treatment) 1mM sodium butyrate and 1 ug/mL doxycycline was added.
|
| Growth protocol |
iSLK-BAC16 (WT) cells were grown in DMEM supplemented with 10% Tet-free FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using TRI-reagent (Molecualr Resarch Center Inc)
One microgram of total RNA per sample was processed with KAPA Stranded RNA-Seq kit with RiboErase (KAPA Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
t24NT_t24P.deseq2.txt
|
| Data processing |
Reads with Phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore (v0.4.1)
Quality-filtered reads were then aligned to the human reference genome hg19, adding KSHV GQ994935.1 as an extra chromosome and using the HISAT (v2.0.1) (13) aligner with default settings.
Duplicates were marked but retained using Sambamba (v0.6.6)
Aligned reads were quantified using featureCounts (v1.4.6) per gene ID against GENCODE GRCh37
Differential gene expression analysis was performed using the R package DEseq2 (v1.6.3)
Assembly: GENCODE GRCh37 (hg19) with GQ994935.1 (KSHV)
Supplementary files format and content: Processed data files are the DEseq2 outputs (as text files) comparing siNT with siPNUTS at each of the four time points
|
| |
|
| Submission date |
Apr 18, 2022 |
| Last update date |
Nov 19, 2022 |
| Contact name |
Nicholas K Conrad |
| E-mail(s) |
nicholas.conrad@utsouthwestern.edu
|
| Phone |
2146480795
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Microbiology
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75063 |
| Country |
USA |
| |
|
| Platform ID |
GPL24095 |
| Series (2) |
| GSE201000 |
The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [RNA-seq] |
| GSE201046 |
The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication |
|
| Relations |
| BioSample |
SAMN27623661 |
| SRA |
SRX14895383 |
