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| Status |
Public on Feb 03, 2017 |
| Title |
LY reactivated SCGs + IFNb, replicate 1 |
| Sample type |
SRA |
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| Source name |
SCG cultures DIV 13-15, harboring reactivating HSV-1
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: superior cervical ganglia
age: E21
reactivation condition: DIV 13-15 SCG cultures reactivated with LY294002 for 20h
ifn type: IFNbeta
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| Treatment protocol |
On DIV 12-14, (6-7 days after HSV-1 infection), ACV was removed and cultures were reactivated with LY294002 (20 μM) for 20 h, in presence or absence of IFNβ or IFNγ (100U/ml).
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| Growth protocol |
Superior cervical ganglia (SCG) neurons isolated from E21 Sprague-Dawley rat pups, cultured in neurobasal medium supplemented with NGF (50 ng/ml) and with aphidicolin (5 mM) and 5-fluorouracil (20 mM) to eliminate proliferating cells. On DIV 5-6, acyclovir (50 mM) was added and 24h later infected with Patton strain HSV-1 EGFP-Us11 at MOI=1. The virus was removed after 2h and the neurons maintained in culture with ACV until reactivation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using Trizol reagent, precipitated with ethanol, DNase-treated, phenol-chloroform extracted, precipitated once more with ethanol and yields determined by absorption spectroscopy using a NanoDrop (NanoDrop Products).
RNA-seq libraries were generated following Illumina TruSeq protocols to remove rRNA using Ribo-Zero, fragmentation, and adaptor ligation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
1277
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| Data processing |
Sequencing reads were aligned using the STAR aligner (v2.5.0a) to the Rnor 6.0 genome (Dobin et al., 2013).
Reads were quantified using featureCounts v1.4.3-p1 (Liao et al., 2014).
Difference analysis of gene expression changes was carried out in R (www.r-project.org; [Ihaka and Gentleman, 1996]) using Bioconductor (Gentleman et al., 2004) and the package edgeR (Robinson and Oshlack, 2010) applying generalized linear model methods to account for biological variation across replicates (McCarthy et al., 2012)
Genome_build: rn6
Supplementary_files_format_and_content: count files of expressed genes used for each pairwise difference analysis, filtered for lowly expressed genes
Supplementary_files_format_and_content: glmEdgeR output files with associated gene name, gene length, and description for pairwise analysis (Reactivated with IFNb; LY+IFNb vs. LY) and (Reactivated with IFNg; LY+IFNg vs. LY)
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| Submission date |
Dec 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mariko Kobayashi |
| E-mail(s) |
[email protected]
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| Organization name |
Rockefeller University
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| Department |
Molecular Neuro-Oncology
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| Lab |
Robert B. Darnell
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| Street address |
1230 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE90744 |
Immune Escape via A Transient Gene Expression Program Enables Productive Replication of A Latent Pathogen |
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| Relations |
| BioSample |
SAMN06093492 |
| SRA |
SRX2388265 |
| 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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