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Sample GSM7400941 Query DataSets for GSM7400941
Status Public on Jun 30, 2023
Title ATF3 knockout A549 cells with ZIKV virus infection, biological replicate 1
Sample type SRA
 
Source name lung epithelial adenocarcinoma
Organism Homo sapiens
Characteristics tissue: lung epithelial adenocarcinoma
cell line: A549
cell type: lung epithelial adenocarcinoma
genotype: ATF3-/-
treatment: ZIKV Infection (10moi)
Treatment protocol Cells were previously seeded to be near 80% confluency on day of infection. Control cells were trypsinized and counted to determine the multiplicity of infection (moi). Cells were infected at an moi of 10. An appropriate aliquot of viral stock was thawed at RT, diluted in PBS to a final volume of 1 ml and added to cells. For mock-infected plates, 1 ml of PBS was added. Cells were incubated at 37 oC for 1 hour, rocking every 15 minutes. An hour later, 9 ml of media was added per plate and returned to the incubator for 24 hours.
Growth protocol A549 cells were cultured in DMEM with 10% fetal bovine serum, 10mM nonessential amino acids, 5mM L-glutamine, and 1% final sodium pyruvate (0.055g/L).
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using TRIzol reagent, followed by clean-up with the RNA Clean and Concentrate Kit (Zymo Research), and DNAse-treated with the TURBO DNA-free kit (invitrogen)
Libraries were constructed by Azenta/Genewiz using polyA+ selection followed by standard Illumina-based RNA-seq library generation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Paired end RNA-seq reads were quantified using kallisto v0.46.2 in quant mode with 100 bootstraps against the Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
Resulting kallisto-derived TPM counts were imported into the R statistical computing enrvironment using tximport, followed by differential gene expression analysis via DEseq2
Assembly: ENSEMBL homo sapies v104 transcriptome release
Supplementary files format and content: ab-separated value files containing standardized ENSMBL gene name, gene length, estimated tag counts, and transcripts per million (TPM) values; output from Kallisto that was imported into DEseq2 via tximport.
 
Submission date May 21, 2023
Last update date Jun 30, 2023
Contact name Morgan A Sammons
E-mail(s) masammons@albany.edu
Organization name University at Albany - SUNY
Department Biological Sciences
Lab Sammons
Street address 1400 Washington Ave, Life Sciences 2075
City Albany
State/province NY
ZIP/Postal code 12222
Country USA
 
Platform ID GPL21290
Series (1)
GSE233049 ATF3- and ZIKV-dependent transcriptome of A549 cells
Relations
BioSample SAMN35299086
SRA SRX20461315

Supplementary file Size Download File type/resource
GSM7400941_ATF3KO_ZIKV_1_abundance.tsv.gz 2.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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