NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5049002 Query DataSets for GSM5049002
Status Public on Apr 14, 2021
Title HCT-116- 4hpi-VACV-WR -replicate 1 [PAR_BC_4hpi_1]
Sample type SRA
 
Source name HCT-116- 4hpi-VACV-WR
Organism Homo sapiens
Characteristics cell line: HCT-116
cell type: Colon cancer cells
genotype: wild type
treatment: Vaccinia WR 4 hrs post infection
Treatment protocol vaccinia virus was added at an MOI=5 and incubated for the indicated time before cells were harvested
Growth protocol Cells were grown in DMEM ((high glucose, pyruvate and L-Glutamine) media supplemented with 10% FBS and maintained in humidified incubator supplied with 5% CO2 atmosphere
Extracted molecule total RNA
Extraction protocol Cells were harvested by trypsinization and total RNA was extracted using TriZol reagent
Total RNA depleted of Ribosomal RNA using Ribozero was converted to cDNA and single read 75 bp library was sequenced on Illumina Hi-Seq instrument (IGM core UCSD)
RNA-Seq depleted of rRNA using ribozero kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description C1_WT_VaccV_4h_1_S7
Data processing Illumina Casava1.7 software used for basecalling.
The demultiplexed and de-indexed Fastq files were processed using galaxy platform @usegalaxy.org
Fastq files were aligned to the Human genome using HISAT2 ()
BAM files from HISAT2 were used to count gene features using Featurecounts
Output from Featurecounts were used as input for DeSEQ2 to identify differentially expressed gene
Genome_build: Hg38
Supplementary_files_format_and_content: Tab delimited text file shows output from Featurecounts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Jan 28, 2021
Last update date Apr 14, 2021
Contact name Elayanambi Sundaramoorthy
Organization name University of California San Diego
Department Section of cell and developmental biology
Lab Bennett lab
Street address 9500, GILMAN DRIVE, la jolla
City san diego
State/province California
ZIP/Postal code 92037
Country USA
 
Platform ID GPL11154
Series (1)
GSE165732 Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection
Relations
BioSample SAMN17616359
SRA SRX9971395

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap