Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of mouse splenocytes following infection with Listeria monocytogenes

ABSTRACT: C57BL/6 mice were maintained in specific pathogen-free conditions in accordance with the Institutional Animal Care and Use Committee. Listeria monocytogenes (clinical isolate 10403s) was from V. Boyartchuk (NTNU, Trondheim, Norway) and infected as previously described (PMID 24477914) for 24 hours before harvesting the spleen. PBS was used as control. . Single cell suspensions from spleens were used to make total RNA. 4 Î¼g of total RNA was used to generate libraries for RNA-sequencing (Illumina unstranded mRNA kits). Samples were sized, quantified and validated on a Bioanalyzer. Libraries were sequenced on a High-Seq System (Illumina 2000, San Diego, CA) as paired-end 100 reads. Sequence reads were aligned to the mouse genome (assembly NCBI m37/mm9) using TopHat.Gene level read counts based on the resulting alignments were calculated using HTSeq. The DESeq R package was used to normalize gene counts, calculate fold change in gene expression, estimate p-values and adjusted p-values for change in gene expression values, and to perform a variance stabilized transformation on read counts.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus domesticus

SUBMITTER: Daniel Caffrey

PROVIDER: E-MTAB-3315 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cutting Edge: A Natural Antisense Transcript, AS-IL1α, Controls Inducible Transcription of the Proinflammatory Cytokine IL-1α.

Chan Jennie J Atianand Maninjay M Jiang Zhaozhao Z Carpenter Susan S Aiello Daniel D Elling Roland R Fitzgerald Katherine A KA Caffrey Daniel R DR

Journal of immunology (Baltimore, Md. : 1950) 20150715 4

Natural antisense transcripts (NATs) are a class of long noncoding RNAs (lncRNAs) that are complementary to other protein-coding genes. Although thousands of NATs are encoded by mammalian genomes, their functions in innate immunity are unknown. In this study, we identified and characterized a novel NAT, AS-IL1α, which is partially complementary to IL-1α. Similar to IL-1α, AS-IL1α is expressed at low levels in resting macrophages and is induced following infection with Listeria monocytogenes or s ...[more]

PMID: 26179904

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Dataset Information

RNA-seq of mouse splenocytes following infection with Listeria monocytogenes

Publications

Cutting Edge: A Natural Antisense Transcript, AS-IL1α, Controls Inducible Transcription of the Proinflammatory Cytokine IL-1α.

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