GEO DataSets

(Submitter supplied) The in vivo role of a novel domain in Swi2/Snf2 required for its function was investigated using microarray analysis.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL739

4 Samples

Download data: GPR

(Submitter supplied) Aberrant forms of the SWI/SNF chromatin remodeling complex are associated with human disease. Loss of the Snf5 subunit of SWI/SNF is a driver mutation in pediatric rhabdoid cancers and forms aberrant sub-complexes that are not well characterized. We determined the effects of loss of Snf5 on the composition, nucleosome binding, recruitment and remodeling activities of yeast SWI/SNF. The Snf5 subunit interacts with the ATPase domain of Snf2 and forms a submodule consisting of Snf5, Swp82 and Taf14 as shown by mapping SWI/SNF subunit interactions by crosslinking-mass spectrometry and subunit deletion followed by immunoaffinity chromatography. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: TXT

(Submitter supplied) Acetylation of Snf2 regulates Swi/Snf recruitment during stress

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17143 GPL13821

56 Samples

Download data: BW

(Submitter supplied) Loss of Swi/Snf subunits regulate transcription.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17342

48 Samples

Download data: BW

(Submitter supplied) Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit. Despite being a ubiquitous component of the complex, physiological roles for this domain remain undefined. Here we show that disruption of ARID1a-DNA binding in mice results in embryonic lethality, with mutant embryos manifesting prominent defects in the heart and extraembryonic vasculature. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

12 Samples

Download data: TXT

(Submitter supplied) The chromatin remodelers (CRs) SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the -1 and +1 nucleosomes flanking NDRs; however, Ino80C’s function in transcriptional activation in vivo is not well understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23014

101 Samples

Download data: BW

(Submitter supplied) Total H4 and acetyl H4 IP, time course Total H4 and acetyl H4 occupancy, Snf2 occupancy, gene expression analysis Keywords: stress response, time course

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array; Expression profiling by array

Platform:

GPL5076

167 Samples

Download data: GPR

(Submitter supplied) We have carried out ChIP-seq to study the distribution of Brahma in the genome of S2 cells and to identify the Brahma-bound genes. We have also knocked down Brahma by RNA interference and we have carried out RNA-seq to determine the changes induced by Brahma depletion in the transcriptome of S2 cells. Furthermore, we have carried out RNA-seq experiments to profile S2 cells in which we first deplete Brahma by RNA interference and then express recombinant Brahma (either wild-type or ATPase mutant). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

12 Samples

Download data: TXT

(Submitter supplied) We did transcription profiling on the effect of rlm1 (MAPK Slt2 transcription factor) deletion and swi3 (component of SWI/SNF complex involved in chromatin remodeling) deletion in genes involved in cell wall stress (Congo Red) response.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

18 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13972

21 Samples

Download data: TXT

(Submitter supplied) ChIP-chip assays to determine the localization of TAP-protein in wild-type and tagging yeast.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13972

12 Samples

Download data: TXT

(Submitter supplied) ChIP-chip assays to determine the localization of Snf5 in wild-type and knockout yeast.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13972

9 Samples

Download data: TXT

(Submitter supplied) Despite its streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae. One of the most striking is the regulated splicing of meiotic transcripts, part of the dramatic reprogramming of gene expression upon meiotic onset. Here we show a crucial role for the chromatin remodeler Snf2, part of the Swi/Snf complex in meiotic regulation of splicing. We find that the complex affects meiotic splicing in several ways. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: XLSX

(Submitter supplied) ATP-dependent chromatin remodelers are commonly mutated in human cancer. Mammalian SWI/SNF complexes comprise three conserved multi-subunit chromatin remodelers (cBAF, ncBAF and PBAF) that share the BRG1 (also known as SMARCA4) subunit responsible for the main ATPase activity. BRG1 is the most frequently mutated Snf2-like ATPase in cancer. Here we have investigated the role of SWI/SNF in genome instability, a hallmark of cancer cells, given its role in transcription, DNA replication and DNA damage repair. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machineries that establish and maintain chromatin accessibility and gene expression by regulating chromatin structure. However, how the remodeling activities of SWI/SNF complexes are regulated in eukaryotes remains elusive. B-cell lymphoma/leukemia protein 7A/B/C (BCL7A/B/C) have been reported as subunits of SWI/SNF complexes for decades in animals and recently in plants; however, the role of BCL7 subunits in SWI/SNF function remains undefined. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

10 Samples

Download data: BIGWIG

(Submitter supplied) Switch defective/sucrose non-fermentable (SWI/SNF) complexes are evolutionarily conserved multi-subunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes remain undefined. more...

Organism:

Arabidopsis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27784

26 Samples

Download data: BED, BIGWIG, NARROWPEAK

(Submitter supplied) Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machineries that establish and maintain chromatin accessibility and gene expression by regulating chromatin structure. However, how the remodeling activities of SWI/SNF complexes are regulated in eukaryotes remains elusive. B-cell lymphoma/leukemia protein 7A/B/C (BCL7A/B/C) have been reported as subunits of SWI/SNF complexes for decades in animals and recently in plants; however, the role of BCL7 subunits in SWI/SNF function remains undefined. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

20 Samples

Download data: BED, BIGWIG

(Submitter supplied) Purpose：Examination of global gene expression of 14-day-old WT, bcl7a(brip3), bcl7b(brip4), bcl7a bcl7b(brip3 brip4), bcl7a bcl7b brm-3(brip3 brip4 brm-3) and bcl7a bcl7b brm-1(brip3 brip4 brm-1) seedlings under short day condition. Methods: Total RNA was extracted from 14-day-old Arabidopsis seedlings under short-day conditions using TRIzol reagent (Invitrogen) following the manufacturer's instructions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

24 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26208 GPL27784

42 Samples

Download data: BED

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: RNA from 14-day-old seedlings of wild-type, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 was isolated using the RNAprep Pure Plant Kit as described above. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT