|
| Status |
Public on Apr 14, 2021 |
| Title |
HCT-116- 8hpi-VACV-WR -replicate 3 [PAR_BC_8hpi_3] |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116- 8hpi-VACV-WR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-116
cell type: Colon cancer cells
genotype: wild type
treatment: Vaccinia WR 8 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 |
E3_WT_VaccV_8h_3_S15
|
| 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 |
SAMN17616351 |
| SRA |
SRX9971403 |
