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SRP030404
Drosophila melanogaster
8 Downloadable Samples
Illumina HiSeq 1000
Description
Transcription and pre-mRNA alternative splicing are highly regulated processes that play major roles in modulating eukaryotic gene expression. It is increasingly apparent that other pathways of RNA metabolism, including small RNA biogenesis, can regulate these processes. However, a direct link between alternative pre- mRNA splicing and small RNA pathways has remained elusive. Here we show that the small RNA pathway protein Argonaute-2 (Ago-2) regulates alternative pre-mRNA splicing patterns of specific transcripts in the Drosophila nucleus using genome-wide methods in conjunction with RNAi in cell culture and Ago-2 deletion or catalytic site mutations in Drosophila adults. Moreover, we show that nuclear Argonaute-2 binds to specific chromatin sites near gene promoters and negatively regulates the transcription of the Ago-2-associated target genes. These transcriptional target genes are also bound by Polycomb group (PcG) transcriptional repressor proteins and change during development, implying that Ago-2 may regulate Drosophila development. Impor- tantly, both of these activities were independent of the catalytic activity of Ago-2, suggesting new roles for Ago-2 in the nucleus. Finally, we determined the nuclear RNA-binding profile of Ago-2, found it bound to several splicing target transcripts, and identified a G-rich RNA-binding site for Ago-2 that was enriched in these transcripts. These results suggest two new nuclear roles for Ago-2: one in pre-mRNA splicing and one in transcriptional repression. Overall design: 2 Ago2 mutants, 51B and V966M, heterozygotes and homozygotes of both each sequenced in duplicate
Publication Title
Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression.
Sample Metadata Fields
Sex, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The present study was designed to identify Mkl1 target genes whose expression requires either the B1 site of Mkl1 and serum response factor (SRF), respectively, or the SAP domain of Mkl1. For this purpose, we obtained the transcriptomes of four stable 4T1 cell lines that either overexpress full length Mkl1-RFP (4T1-FL), Mkl1-RFP with a mutated SRF-interaction site (4T1-mutB1), Mkl1-RFP with a deletion of the SAP domain (4T1-SAP) or an empty vector encoding RFP alone (4T1 control).
Publication Title
Mechanism of irradiation-induced mammary cancer metastasis: A role for SAP-dependent Mkl1 signaling.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The present study was designed to identify genes induced by irradiation in the 4T1 breast cancer model mimicking aggressive local relapse after radiotherapy. For this purpose, we obtained the transcriptomes of 4T1 tumors grown in either preirradiated (IRR+4T1) or non-irradiated (4T1) mammary tissue.
Publication Title
Mechanism of irradiation-induced mammary cancer metastasis: A role for SAP-dependent Mkl1 signaling.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Analysis of different iPSC clones in comparison to parental fibroblasts and Pluripotent ESC and iPSC lines
Publication Title
CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We have previously shown that HC11 mammary epithelial cells react strongly to the overexpression of megakaryoblastic leukemia-1 (Mkl1) with induction of tenascin-C expression. The present study was designed to find genes co-regulated with tenascin-C by Mkl1 in a SAP domain-dependent manner and without the involvement of serum response factor (SRF). For this purpose, we compared the transcriptomes of three stable HC11 cell strains that either overexpress full length Mkl1-RFP (HC11-FL), Mkl1-RFP with a mutated SRF-interaction site (HC11-mutB1) or Mkl1-RFP with a deletion of the SAP domain (HC11-SAP).
Publication Title
SAP domain-dependent Mkl1 signaling stimulates proliferation and cell migration by induction of a distinct gene set indicative of poor prognosis in breast cancer patients.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
SV7tert AML cells were obtained from ATCC and cultured in Dulbecco's modified essential medium (DMEM), glutamine (4mmol) and 10% foetal bovine serum (FBS). Two million SV7tertAML cells were subcutaneously injected into nude mice either with or without subcutaneous oestrogen pellets (n=4 per group); oestrogen was added using 0.36mg 60 day release oestrogen pellets implanted sub-cutaneously. Mice were housed in pathoflex isolators at 26C, on 12 hour light / dark cycles. Irradiated RB2 diet and autoclaved water provided ad libertum.
Publication Title
Analysis of the oestrogen response in an angiomyolipoma derived xenograft model.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
Analysis of the gene signature of steatosis associated to obesity in hepatocytes of Zucker fa/fa obese rats and their controls; identifying target genes linked to steatosis progression. or Obesity and insulin resistance-associated steatosis can be a non-inflammatory condition affecting hepatocytes or progress to steatohepatitis: a condition that can result in end-stage liver disease. Although molecular events leading to accumulation of lipid droplets in the liver have been identified individually, the complexity of the condition suggested that emergent target would be uncovered by a more comprehensive examination. Then, this study was aimed at establishing a gene signature of steatosis in hepatocytes and at identifying target genes linked to steatosis progression. Using Affymetrix oligonucleotide arrays, we compared transcriptomes of hepatocytes isolated from Zucker "fa/fa" obese rats with three different age-related grades of steatosis with those of their counterpart non-steatotic cells.
Publication Title
A subset of dysregulated metabolic and survival genes is associated with severity of hepatic steatosis in obese Zucker rats.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 882 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 882 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, the Novartis Institutes for Biomedical Research and the Genomics Novartis Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models
Publication Title
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.
Publication Title
Transcriptomic Analysis of Mouse Cochlear Supporting Cell Maturation Reveals Large-Scale Changes in Notch Responsiveness Prior to the Onset of Hearing.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples