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Status |
Public on Jun 30, 2018 |
Title |
12hrs control_2 |
Sample type |
SRA |
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Source name |
Vero cell line
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Organism |
Chlorocebus aethiops |
Characteristics |
treatment: control cell line: vero
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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.
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Growth protocol |
Vero cells from three different time points(12hr,24hr, 48hr) were used.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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.
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Submission date |
Jun 30, 2016 |
Last update date |
May 15, 2019 |
Contact name |
vineela gangalapudi |
E-mail(s) |
vineela.gangalapudi@cshs.org
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Organization name |
Cedars- sinai Medical center
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Department |
Biomedical sciences
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Lab |
Genomics Core
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Street address |
8723 Alden drive
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City |
Los Angeles |
State/province |
CALIFORNIA |
ZIP/Postal code |
90048 |
Country |
USA |
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Platform ID |
GPL22096 |
Series (1) |
GSE83900 |
Dysregulation of long non-coding RNA genes during ZIka virus Infection |
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Relations |
BioSample |
SAMN05330344 |
SRA |
SRX1888450 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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