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Sample GSM6048392 Query DataSets for GSM6048392
Status Public on Nov 19, 2022
Title Rep3 t0 siNT
Sample type SRA
 
Source name iSLK-BAC16 (WT)
Organisms Homo sapiens; Human gammaherpesvirus 8
Characteristics cell type: iSLK cells
virus: BAC16 infectious clone
treatment: siNT
induction: none
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 t0NT_t0P.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 SAMN27623674
SRA SRX14895370

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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