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Sample GSM7317554 Query DataSets for GSM7317554
Status Public on May 15, 2023
Title RCMV_Input_3
Sample type SRA
 
Source name spleen
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley rats
tissue: spleen
cell type: Dendritic cells
treatment: none
timepoint: N/A
Treatment protocol DCs were enriched from spleen homogenates using OX-62 (CD103) microbeads (Miltenyi Biotec), and RNA was either directly extracted after enrichment or 24h hours later following infection with wt/∆vXLC1/UV-irradiated rat CMV at an MOI of 3 or mock infection, as indicated.
Growth protocol Sprague Dawley rats were bred at the animal facility of the Robert Koch Institute and sacrificed by an isoflurane overdose.
Extracted molecule polyA RNA
Extraction protocol Cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description polyA enrichment
Data processing Sequencing reads were aligned to the rn6 version of the rat genome using hisat2 (Kim et al, 2015) with standard parameters.
Reads were then quantified using quasR (Gaidatzis et al, 2015).
Assembly: rn6
Supplementary files format and content: tab-separated values
 
Submission date May 10, 2023
Last update date May 15, 2023
Contact name Emanuel Wyler
E-mail(s) emanuel.wyler@mdc-berlin.de
Phone +49 30 9406 3009
Organization name Max Delbrück Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Lab RNA Biology and Posttranscriptional Regulation
Street address Robert Roessle Str 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platform ID GPL22396
Series (1)
GSE232184 Rat cytomegalovirus efficiently replicates within dendritic cells and affects both surface marker and gene expression
Relations
BioSample SAMN35026861
SRA SRX20281048

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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