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Homo sapiens
6 Downloadable Samples
Illumina Genome Analyzer IIx
Description
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. Overall design: CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized relative to Rabbit Ig control IP-seq reads. RNA-seq was performed in BJAB and BL41 cells transduced with shRNA against CTCF or RFP as a control, and in untransduced cells as well.
Publication Title
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
HnRNPLL was identified as a critical regulator of CD45 alternative splicing in a lentiviral shRNA screen. RNAi-mediated depletion of hnRNPLL eliminated the activation-induced induced transition from the CD45RA to the CD45RO isoform. HnRNPLL is induced during the process of T cell activation, raising the possibility that it regulates a broad program of alternative splicing in activated T cells. To test this possibility and to identify additional potential targets of hnRNPLL, we performed exon array analysis on RNA isolated from five cellular conditions: 1) activated peripheral CD4+ T cells, 2) peripheral CD4+ T cells infected with a control shRNA directed against GFP, 3) peripheral CD4+ T infected with an shRNA directed against hnRNPLL, 4) nave cord blood CD4+ T cells, and 5) cord blood CD4+ T cells that had been activated with anti-CD3 and anti-CD28 for 24 hours. The RNA was hybridized to Affymetrix human exon arrays and the hybridization signals were analyzed with XRAYTM software (Biotique). Using stringent filters for non-expressed probesets, we identified 132 genes that showed significant alternative exon usage (p<0.01) in response to hnRNPLL knockdown, but not in response to shGFP infection. Of these 132 genes, 36 also showed significant alternative exon usage in response to activation of cord blood cells, which results in an approximate 5-fold increase in hnRNPLL expression. We thus conclude that induction of hnRNPLL represents a mechanism by which cells can rapidly shift their transcriptomes during the process of T cell activation.
Publication Title
Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
In order to identify genes with differential gene expression or alternative splicing between the groups LL-sh4, uninfected, and shGFP we study 6 hybridizations on the Human Exon 1.0 ST array using mixed model analysis of variance. 842 genes with significant gene expression differences between the groups and 1118 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 192 genes with both gene and possible splicing differences (p<0.01). Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes (p<0.01).
Publication Title
Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE11832- Homo sapiens
- 2 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
In order to identify genes with differential gene expression or alternative splicing between the groups naive and activated we study 4 hybridizations on the Human Exon 1.0 ST array using mixed model analysis of variance. 1904 genes with significant gene expression differences between the groups and 1603 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 427 genes with both gene and possible splicing differences (p<0.01). Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes (p<0.01).
Publication Title
Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
CD138+ B220- plasma cells were sorted from bone marrow and B220+ CD23+ mature follicular B cells were sorted from the spleens. Plasma cells were sorted from C57BL/6 mice 7 days after boosting with antigen, with mice first primed with an i.p. injection of KLH/IFA followed by boost at day 21 with KLH/PBS i.p. Mature B cells were sorted from antigen-nave C57BL/6 mice.
Publication Title
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Aging is associated with major nuclear changes affecting genomic integrity and gene expression. Here we compare the gene expression profiles in the neocortex of young (5 months old) and old (30 months old) B6xC3 F1 mice.
Publication Title
SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
We have determined that verticillin A is a histone methyltransfease inhibitor that selectively inhibits human SUV39H1, SUV39H2, G9a and GLP to inhibit H3K9 methylation in human colon cancer cells. The objective here is to identify verticillin A target genes in human colon cancer cells.
Publication Title
H3K9 Trimethylation Silences Fas Expression To Confer Colon Carcinoma Immune Escape and 5-Fluorouracil Chemoresistance.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Silymarin (SM) is a popular botanical medicine with purported liver protective effects. SM displays multiple effects in animal models and in cell culture including prevention of liver disease, reduction of inflammation, oxidative stress, and proliferation. Despite a plethora of data indicating that SM impinges on multiple cellular signaling pathways important in inflammation and disease, no unifying mechanisms have been forwarded. To define how SM elicits so many biological effects, the current study presents the first comprehensive transcriptional profiling study of human hepatoma cells treated with SM. The intention of the study was to focus on the early transcriptional events that are associated with SM-induced inhibition of proliferation and inflammation. Collectively, the data demonstrate that SM causes a rapid transcriptional reprogramming of cells that initially manifests as energy stress and slowing of cellular metabolism, leading to inhibition of cell growth and inflammation.
Publication Title
Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Time
View Samples- Homo sapiens
- 40 Downloadable Samples
- Illumina HiSeq 2000
Description
We studied changes in a whole transcriptome during dsDNA virus infection. Overall design: Fibroblasts (MRC5 & HFF) and epithelial cells (ARPE19) were infected with HCMV, HSV1 or Ad5 and total RNA was isolated at 48, 9, or 24 hpi, respectively. Total 15 treatments were used. There were 2 biological replicates analyzed per each treatment.
Publication Title
A tumor-specific endogenous repetitive element is induced by herpesviruses.
Sample Metadata Fields
Specimen part, Subject
View Samples