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Homo sapiens
16 Downloadable Samples
IlluminaHiSeq2000
Description
The purpose of this study was to profile gene expression changes that could occur with the loss of co-repressor SLIRP. In addition, we wanted to investigate how DHT could further alter gene expression. Methods: LNCaP cells were transfected with custom nonsense control siRNA or a pool of SLIRP siRNA (HSS130109, HSS188666, HSS188667 Invitrogen, Carlsbad, CA) at 40nM for 24hrs. Cells were washed once with PBS and replaced with SFM containing EtOH or 1nM/ml DHT for another 24hrs. Two biological replicates were collected from 2 different experiemnts for total of 4 replicates. RNA collected was sequenced using Illumia HiSeq2000 single read 50 bp by the HTSF core at UNC and aligned and normalized by the Bioinformatics core at UNC. Results: We found a differential gene expression pattern between our control and SLIRP knockdown samples. We also identified a 176 AR gene signature with 3 subclasses and a large SLIRP gene signature (~1700). Overall design: Examination of control (NS) vs. SLIRP siRNA treated with 1nM DHT in the prostate cancer cell line LNCaP
Publication Title
Interaction between androgen receptor and coregulator SLIRP is regulated by Ack1 tyrosine kinase and androgen.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 78 Downloadable Samples
- Illumina HiSeq 2500
Description
To determine the role of Mbd3/NuRD in lymphopoiesis, gene expression in purified populations of Mbd3-deleted and control lymphoid progenitor cells was analysed using RNA-seq. Overall design: Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow by flow cytometry, including haematopoietic stem cells (HSCs), lymphoid-primed multipotent progenitors (LMPPs), all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs). RNA-seq was performed on 100 HSCs or 150 cells from the other populuations, using the previously described smartseq2 protocol for RNA-seq of small numbers of cells (Picelli et al. (2014) Nature protocols 9:171).
Publication Title
Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
The process of lung squamous carcinoma tumorigenesis and metastasis is poorly characterized. Additionally, few models of this process exist in an immune-competent context. In order to address this problem, we utilized the KLN-205 lung squamous carcinoma cell lines that is derived from carcinogen exposure in DBA2 mice.
Publication Title
Factor XIIIA-expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 25 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour interval across 2 circadian cycles, cells from single 6-well plates were harvested and pooled for total RNA extraction.
Publication Title
Circadian profiling of the transcriptome in immortalized rat SCN cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 36 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 36 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Transcriptomics of distinct subpopulations of synovial fibroblasts from osteoarthritis and rheumatoid arthritis arthroplasty tissues.
Publication Title
Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis.
Sample Metadata Fields
Sex, Age, Disease
View Samples
SRP032280- Homo sapiens
- 1 Downloadable Sample
- IlluminaGenomeAnalyzerII
Description
RNAseq to determine baseline expression of kinome in MDA-MB-231 claudin-low breast cancer cell line
Publication Title
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples SRP032344- Homo sapiens
- 1 Downloadable Sample
- IlluminaGenomeAnalyzerII
Description
RNAseq of SUM159PT claudin-low breast cancer cell line to determine baseline kinome expression
Publication Title
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 47 Downloadable Samples
- Illumina Genome Analyzer II
Description
Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq. Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling, were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating that a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling. Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long-term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress. Overall design: Examination of a time course (day 0, 1, 2 and 7) for 2 treatments, calves either housed with their dam (control) or housed and simultaneously weaned, using RNA-seq. The supplementary processed data file 'read_counts.txt' contains unnormalized read counts for each Ensembl bovine gene in each of the 48 samples. Unnormalized counts are required for input to EdgeR. Genome build: Btau4.0
Publication Title
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.
Sample Metadata Fields
Specimen part, Disease, Treatment, Subject
View Samples- Mus musculus
- 27 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
To screen for specific circadian outputs that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared to that found in the rat SCN in vivo and SCN2.2 cells in vitro. Similar to the scope of circadian gene expression in SCN2.2 cells and the rat SCN, NIH/3T3 fibroblasts exhibited circadian fluctuations in the expression of the core clock genes, Per2, Bmal1 (Mop3), and Cry1 and 323 functionally diverse transcripts (2.6%), many of which were involved in cell communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among cellular pathways mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase, the enzyme responsible for the production of nitric oxide, in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that this gaseous neurotransmitter may play a key role in SCN pacemaker function. Thus, this comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective identification of circadian signals involved in the coupling of SCN oscillators and the regulation of rhythmicity in downstream cells or tissues.
Publication Title
Circadian profiling of the transcriptome in NIH/3T3 fibroblasts: comparison with rhythmic gene expression in SCN2.2 cells and the rat SCN.
Sample Metadata Fields
No sample metadata fields
View Samples