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SRP075430
Homo sapiens
2 Downloadable Samples
Illumina HiSeq 2500
Description
In order to validate our method to develop immortalized cellular models of microglia, we used RNA-seq to confirm the microglial phenotype of a representative clone (C20, a clonal population), which derived from the transformation of human primary microglia (human microglia purchased cryopreserved after purification from Sciencell, Cat. #1900). Transformation was carried out with vesicular stomatitis virus G envelop simian virus 40 large T antigen viral particles (VSVG SV40), containing the pBABE-puro SV40 LT construct (Addgene, Plasmid #13970), followed by VSVG containing the human telomerase reverse transcriptase (hTERT)-neomycin (pBABE-neo-hTERT) construct (Addgene, Plasmid #1774). Immortalized cells were selected in the presence of 2 µg/mL puromycin and 600 µg/mL neomycin. Individual clonal populations, including clone C20, were allowed to grow for approximately 4 weeks prior to further testing. In addition, we also used RNA-seq to verify the capacity of these cellsto respond to an inflammatory stimulus (TNF-a).
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 32 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
In the current study, we investigated the collective roles of protein tyrosine phosphatases (PTPs) and histone deacetylases (HDACs) on regulation of IRG expression in human choriocarcinoma cells by genome-wide transcriptional profiling. Logic-rules were optimized to derive rules governing gene expression patterns observed upon different combinations of treatment with PTP and HDAC inhibitors. The data reveal that IRGs can be divided into distinct subsets that are differentially modulated by co-treatment of Jar cells with IFN-? and PTP versus HDAC inhibitors, respectively. Furthermore, promoter analysis of the genes governed by the rules identifies transcription factor binding sites associated with the different gene subsets. Thus, the regulatory modes identified in this study provide insights into the complex regulation of inflammatory pathways at the fetal-maternal interface, as well as mechanisms that choriocarcinoma cells may utilize to promote their survival.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 32 Downloadable Samples
- Illumina HiSeq 2500
Description
Retinoic acid-inducible gene-I (RIG-I) is a cytosolic pathogen recognition receptor that initiates the innate immune response against many RNA viruses. RIG-I also has been shown to sense some DNA viruses, and host RNA polymerase III (RNA Pol III), a cytosolic DNA sensor, converts cytosolic AT-rich DNA into RNA to be sensed by RIG-I. We previously showed that the RIG-I restricts Kaposi Sarcoma-associated herpesvirus (KSHV) reactivation (J Virol. 2014 May;88(10):5778-87). In this study, we report that KSHV stimulates the RIG-I signaling pathway in an RNA Pol III-independent manner and subsequently induces type I IFN responses. Knockdown or inhibition of RNA Pol-III had no effect on IFN-ß induction by KSHV. By using CLIP (Cross-Linking and Immunoprecipitation) and RNA deep sequencing technologies, we identified multiple KSHV regions that give rise to RNA fragments binding to RIG-I, such as ORF810420-10496, ORF6411058-110675, Repeat region (LIR1)119059-119204, and ORF2543561-43650. The sequence dissimilarity between these fragments suggests that RIG-I detects a particular structure rather than a specific sequence motif. Synthesized ORF810420-10496 RNA stimulated RIG-I-dependent but RNA Pol III-independent IFN-ß signaling. In summary, some KSHV viral RNAs are sensed by RIG-I in an RNA Pol III-independent manner.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line, Treatment, Race
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- NextSeq 500
Description
Fresh splenic Treg cells (CD4+CD25+YFP+) were isolated from 6-week-old Senp3+/+Foxp3-Cre and Senp3fl/flFoxp3-Cre mice and stimulated with anti-CD3 and anti-CD28 for 24 hours. Activated Treg cells were used for total RNA isolation with TRIzol and subjected to RNA-sequencing.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Mus musculus
- 5 Downloadable Samples
- NextSeq 500
Description
Single NG2-glia with GFP fluorescence labeling from PDGFRaCreER; mGFP mice was selected and aspirated into a glass pipette from hippocampal acute slices. In brief, cells were picked promptly by micromanipulation and immediately placed in lysis buffer. All NG2 glial cells were collected within 3 h after slice preparation. The selected NG2-glia were processed for single-cell RNA extraction and reverse transcription within 1 h and were subjected to RNA-sequencing.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- NextSeq 500
Description
B cell mRNA profiles of 18-week-old wild type (WT) and B cell-specific SHIP1 knockout (SHIP?B) mice were generated by deep sequencing, in duplicate, using Illumina Nextseq500.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Danio rerio
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi, using zebrafish and the fungus Mucor circinelloides as host and pathogen model, respectively. Total RNA was sequenced (RNA-seq) from abdominal organs of infected fish.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Ion Torrent Proton
Description
Actively proliferating cells must constantly monitor and re-adjust their metabolic pathways to ensure phospholipid homeostasis for the replenishment of membranes and intracellular trafficking. Multiple studies have suggested that the lysine acetyltransferase NuA4 has a role in fine-tuning phospholipid metabolism in Saccharomyces cerevisiae, however the role of NuA4 in phospholipid homeostasis remains poorly defined. NuA4 mutants have increased gene expression of inositol-3-phosphate synthase, INO1 and overproduce inositol. NuA4 mutants are also display synthetic sickness with a mutant of the lipid remodeling gene SEC14. Here using a combination of genetics and transcriptional profiling, we explore the connections between NuA4, inositol and Sec14. We found that NuA4 mutants exacerbated the inositol auxotrophy of sec14-1ts. Transcriptome studies reveal that loss of the NuA4 subunit EAF1 in sec14-1ts depresses INO1 expression but not all inositol/choline responsive phospholipid genes. This suggests eaf1? cells are defective in coordinating phospholipid homeostasis beyond inositol production. In fact, we discovered that eaf1? cells have significantly lower lipid droplet levels and that inhibition of the fatty acid biosynthesis pathway increased the growth defect of sec14-1ts to a similar extent as untreated sec14-1tseaf1?. Altogether, our work identifies a role for NuA4 as a critical mediator of phospholipid metabolism, potentially as positive regulator of fatty acid biosynthesis.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina HiSeq 1500
Description
The goal was to characterize gene expression profiles of HSPCs in mice during Bordetella pertussis infection. Mice were immunized with acellular or whole cell pertussis vaccines. HSPCs were isolated by flow cytometric sorting and RNA was prepared for library prep and RNA seq analysis.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples