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SRP126061
Mus musculus
14 Downloadable Samples
NextSeq 500
Description
We used RNA sequencing to characterize gene expression of dendritic cells from mouse lymph node that, based on LIPSTIC labeling, underwent interaction with CD4+ T cells. Overall design: Antigen pulsed dendritic cells (DCs) were transferred into recipient mice, followed by antigen specific CD4+ T cells. Forty-eight hours after T cell transfer, endogenous dendritic cells were isolated by facs sorting from mouse lymph node and analyzed based on their in vivo LIPSTIC labeling.
Publication Title
Monitoring T cell-dendritic cell interactions in vivo by intercellular enzymatic labelling.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 40 Downloadable Samples
- Illumina HiSeq 2000
Description
In this experiment we profiled the transcriptome of intestinal colonic epithelium and total colonic tissue of animals colonized with T.mu versus naïve littermate controls at different time points Overall design: Groups of three mice were inoculated with 2x106 highly purified Tritrichomonas musculis. Total tissue and epithelial cells were collected at 3 days, 14 days and 48 days after inoculation from three different mice. RNA was isolated and sequenced
Publication Title
Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 21 Downloadable Samples
Illumina MouseRef-8 v2.0 expression beadchip
Description
Innate immunity is fundamental to recognition and clearance of bacterial infection. The relevant cells and molecules that orchestrate an effective response, however, remain incompletely understood. Here we describe a previously unknown population of B cells, which we have named innate response activator (IRA) B cells that recognize bacteria directly through TLR-4-MyD88 and protect against polymicrobial sepsis.
Publication Title
Innate response activator B cells protect against microbial sepsis.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 157 Downloadable Samples
- NextSeq 500
Description
Primary RNAseq data for 103 highly purified immunocyte populations representing all lineages and several differentiation cascades, profiled using the ImmGen ULI pipeline. Overall design: These RNAseq profiles were generated by ImmGen labs in a combined study associating RNAseq and ATACseq performed on cell populations sorted in parallel (companion ATACseq datasets are found in GSE100738). The 103 cell populations include all adaptive and innate lymphocytes (B, abT, gdT, Innate-Like Lymphocytes), myeloid cells (dendritic cells, macrophages, monocytes), mast cells and neutrophils. Most were prepared from baseline unchallenged mice, some after cell activation (LPS, anti-CD3, viral infection). For B and T lymphocytes, many successive steps of their known differentiation cascades in the thymus and bone marrow are included. ---------------------------------------- Immunological Genome Project Consortium
Publication Title
The cis-Regulatory Atlas of the Mouse Immune System.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 45 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
ZFHX4 and CHD4 suppression independently shift tumor initiating cells out of a stem like state and toward a differentiated morphology.
Publication Title
ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Trans-splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans-splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which integrates different types of high-throughput long-/short-read transcriptome sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing. Combining TSscan screening with multiple experimental validation steps revealed that most chimeric RNA products were platform-dependent experimental artifacts of RNA sequencing. We successfully identified and confirmed four trans-spliced RNAs, including the first reported trans-spliced large intergenic noncoding RNA ("tsRMST"). We showed that these trans-spliced RNAs were all highly expressed in human pluripotent stem cells and differentially expressed during hESC differentiation. Our results further indicated that tsRMST can contribute to pluripotency maintenance of hESCs by suppressing lineage-specific gene expression through the recruitment of NANOG and the PRC2 complex factor, SUZ12. Taken together, our findings provide important insights into the role of trans-splicing in pluripotency maintenance of hESCs and help to facilitate future studies into trans-splicing, opening up this important but understudied class of post-transcriptional events for comprehensive characterization
Publication Title
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Gene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expressing the zinc transporter ZIP8 (SLC39A8) protein.
Publication Title
Pleiotropic roles of metallothioneins as regulators of chondrocyte apoptosis and catabolic and anabolic pathways during osteoarthritis pathogenesis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 250 Downloadable Samples
- Illumina HiSeq 2500, Ion Torrent Proton
Description
The goal of this study is to compare transcriptional profiles of regulatory T cells and conventional CD4 T cells in human breast cancer to regulatory T cells and conventional CD4 T cells in normal breast parenchyma and in peripheral blood. Overall design: RNA sequencing of 2 different cell types in 3 different tissues
Publication Title
Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 53 Downloadable Samples
- Illumina HiSeq 2000
Description
We report global gene expression profilies of Brassinosteroid related Arabidopsis mutants in response to dehydration and fixed-carbon starvation stresses by RNA-seq Overall design: Arabidopsis plants of listed genotypes were grown for 4 weeks under long day (16 hour light) conditions before being subjected to control, 4 hour dehydration, or 5 day fixed carbon starvation treatments.
Publication Title
Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Responses.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 31 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Hair follicles undergo recurrent cycling of controlled growth (anagen), regression (catagen), and relative quiescence (telogen) with a defined periodicity. Taking a genomics approach to study gene expression during synchronized mouse hair follicle cycling, we discovered that, in addition to circadian fluctuation, CLOCK-regulated genes are also modulated in phase with the hair growth cycle. During telogen and early anagen, circadian clock genes are prominently expressed in the secondary hair germ, which contains precursor cells for the growing follicle. Analysis of Clock and Bmal1 mutant mice reveals a delay in anagen progression, and the secondary hair germ cells show decreased levels of phosphorylated Rb and lack mitotic cells, suggesting that circadian clock genes regulate anagen progression via their effect on the cell cycle. Consistent with a block at the G1 phase of the cell cycle, we show a significant upregulation of p21 in Bmal1 mutant skin. While circadian clock mechanisms have been implicated in a variety of diurnal biological processes, our findings indicate that circadian clock genes may be utilized to modulate the progression of non-diurnal cyclic processes.
Publication Title
Circadian clock genes contribute to the regulation of hair follicle cycling.
Sample Metadata Fields
Sex
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