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Sample GSM2221263 Query DataSets for GSM2221263
Status Public on Jun 30, 2018
Title 24hrs control_2
Sample type SRA
 
Source name Vero cell line
Organism Chlorocebus aethiops
Characteristics treatment: control
cell line: vero
Treatment protocol Vero cell line was maintained in DMEM medium which was supplemented in 10% fetal bovine serum (FBS), penicillin (100 units/ml), streptomycin (100 mg/ml), 10 mM Hepes, and 2 mM L-glutamine.The following day, Zika viral inoculum was prepared in serum-free base media at an MOI of 1.
Growth protocol Vero cells from three different time points(12hr,24hr, 48hr) were used.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy Mini Kit (Quiagen)
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with single end 75bp sequencing chemistry.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing We used the STAR aligner to map the samples, and Qced them using Rseqc then used DEseq2 for DE to get the significantly differentially expressed genes between the control and treated samples at each time point
Genome_build: GRCh38 version 23
Supplementary_files_format_and_content: Excel table includes count values for lincRNA and protein-coding genes for each Sample calculated by STAR.
 
Submission date Jun 30, 2016
Last update date May 15, 2019
Contact name vineela gangalapudi
E-mail(s) vineela.gangalapudi@cshs.org
Organization name Cedars- sinai Medical center
Department Biomedical sciences
Lab Genomics Core
Street address 8723 Alden drive
City Los Angeles
State/province CALIFORNIA
ZIP/Postal code 90048
Country USA
 
Platform ID GPL22096
Series (1)
GSE83900 Dysregulation of long non-coding RNA genes during ZIka virus Infection
Relations
BioSample SAMN05330348
SRA SRX1888454

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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