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Saccharomyces cerevisiae
27 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The cohesin acetyltransferase Eco1 coordinates rDNA replication and transcription.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 27 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Eco1 is an acetyltransferase subunit of the cohesin complex and acts during DNA replication to establish cohesion between sister chromatids. However, cohesin has additional functions in gene expression, DNA damage repair, and higher-order organization of chromosomes. The eco1 mutant W216G disrupts acetyltansferase activity, and causes genome-wide transcriptional defects which can be suppressed by deletion of FOB1, a gene also involved in DNA replication. This experiment investigates gene expression differences between the eco1-W216G mutant, and mutants in FOB1, and RAD61 a gene involved in inhibition of cohesion establishment but mutation of which is able to suppress temperature sensitivity of the eco1-W216G mutant.
Publication Title
The cohesin acetyltransferase Eco1 coordinates rDNA replication and transcription.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
IlluminaHiSeq2000
Description
The development of affinity purification technologies together with mass spectrometric analyses of the purified protein mixtures (AP-MS) has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we have investigated whether ectopic expression of an affinity tagged transcription factor as bait in AP-MS experiments perturbs gene expression in cells resulting in false positive identification of bait associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA-Seq, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then copurify non-specifically and be misidentified as bait associated proteins. Therefore typical controls should be sufficient and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFêB1, NFêB2, Rel, RelB, IêBá, IêBâ and IêBå). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFêB family transcription factors. The work here therefore provides a conceptual and experimental framework for analyzing transcription faction protein interactions. Overall design: Gene expression profiles were assayed in triplicate from HEK293 cells expressing either Halo-RelA, Halo-NFkB1, or Halo tag alone.
Publication Title
Controlling for gene expression changes in transcription factor protein networks.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
This experiment analyzes the set of RNAs copurifying with the protein TNIP2 (amino acids 196-346) Overall design: HEK293 cells were transfected with constructs expressing either Halo tag (controls) or Halo-TNIP2 196-346. Total RNA was purified from an aliquot of the whole cell extract (Input samples). Halo-tagged proteins were purified from the remainder of the whole cell extract, and RNA subsequently purified from the Halo purified samples (Pulldown samples).
Publication Title
TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.
Sample Metadata Fields
Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
The Saccharomyces cerevisiae R2TP protein complex consists of Rvb1, Rvb2, Pih1 and Tah1. The R2TP complex has been implicated in various cellular processes such as assembly of snoRNP complex, RNA polymerase II complex, apoptosis and PIKK signaling. The involvement of R2TP in assembling various complexes seems to be in part due to Pih1 and Tah1, which serve as adapter/recruiter proteins. Here, we have performed high resolution RNA-seq. analyses to identify differential expression levels between wild type and PIH1 and TAH1 deletion strains of Saccharomyces cerevisiae that can help in unraveling other functions of Pih1 and Tah1. Both wild type and deletion strains contained TAP (tandem affinity purification) tag at the C-terminal end of either RVB1 or RVB2. Overall design: 3 biological replicates were performed for each strains
Publication Title
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 33 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 33 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Transcriptome analysis of mRNA samples purified from developing cerebellar granule cells and ES cell-derived granule cells using translating ribosome affinity purification (TRAP) method.
Publication Title
Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation.
Sample Metadata Fields
Specimen part
View Samples
GSE1825- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Comparison of gene expression profiles between neuroblastoma samples and Ewing family tumor samples. RNA from native tumor samples was processed for DNA-microarray analysis using Affymetrix HG-U133A microarrays. Primary image analysis was performed using MAS 5.0 and data were scaled to an target intesity of 500.
Publication Title
DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-derived cells and define novel targets.
Sample Metadata Fields
No sample metadata fields
View Samples GSE1824- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Gene expression analysis of cell lines initially established as neuroblastoma cell lines. Cells were harvested and processed for DNA-microarray analysis using Affymetrix HG-U133A microarrays. Primary image analysis was performed using MAS 5.0 and data were scaled to an target intesity of 500.
Publication Title
DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-derived cells and define novel targets.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Novel genetic features of human and mouse Purkinje cell differentiation defined by comparative transcriptomics.
Sample Metadata Fields
No sample metadata fields
View Samples