GEO DataSets

Analysis of lin-35 null mutants at the embryonic stage, and L1 and L4 larval stages. LIN-35 is an ortholog of the mammalian pocket protein family members, pRb, p107, and p130. Results provide insight into the role of pocket proteins in development.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, transformed count, 3 development stage, 2 genotype/variation sets

Platform:

GPL200

Series:

GSE6547

18 Samples

Download data: CEL

(Submitter supplied) LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in conjunction with E2F. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS2751

Platform:

GPL200

18 Samples

Download data: CEL

(Submitter supplied) Microarray-based expression profiling of dissected gonads from efl-1, dpl-1 and lin-35 mutants reveals that EFL-1 and DPL-1 promote expression of an extensively overlapping set of target genes, consistent with the expectation that these two proteins function as a heterodimer. Regulatory regions upstream of many of these target genes have a canonical E2F binding site, suggesting that their regulation by EFL-1/DPL-1 is direct. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL3859 GPL3860

10 Samples

Download data

(Submitter supplied) The highly conserved DREAM transcriptional repressor complex contains an RB-like pocket protein, an E2F-DP transcription factor heterodimer, and the 5-subunit MuvB complex. Using CRISPR/Cas9 targeted mutagenesis, we disrupted the interaction between the sole Caenorhabditis elegans pocket protein LIN-35 and the MuvB subunit LIN-52. A triple alanine substitution of LIN-52's LxCxE motif (3A) severed LIN-35-MuvB association and caused classical DREAM mutant phenotypes, including synthetic multiple vulvae, high-temperature arrest, and ectopic expression of germline genes in the soma. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25147

8 Samples

Download data: TXT

(Submitter supplied) The Retinoblastoma-like pocket proteins p130 and p107 act as gatekeepers of the cell cycle through their activity within the DREAM (Dp/Rb-like/E2F/MuvB) transcriptional repressor complex. The goal of this study was to address how the pocket protein contributes to DREAM complex assembly and function on chromatin by utilizing a protein null mutant of the only C. elegans pocket protein LIN-35. We performed ChIP-seq of C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL22765 GPL13657 GPL9269

46 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Our slr-2 dataset showed strong overrepresentation of genes previously identified in a serial analysis of gene expression (SAGE) intestinal library (McGhee et al., 2006) (p << 0.01); 812 genes were common to both data sets. Consistent with the deregulation of intestinal genes, we observed repression of several important metabolic pathways, including the TOR and insulin signaling networks, suggesting that slr-2(ku297) mutants experience metabolic stress. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

6 Samples

Download data: CEL

(Submitter supplied) The mammalian Retinoblastoma (RB) family including pRB, p107, and p130 represses E2F target genes through mechanisms that are not fully understood. In D. melanogaster, RB-dependent repression is mediated in part by the multisubunit protein complex Drosophila RBF, E2F, and Myb (dREAM) that contains homologs of the C. elegans synthetic multivulva class B (synMuvB) gene products. Using an integrated approach combining proteomics, genomics, and bioinformatic analyses, we identified a p130 complex termed DP, RB-like, E2F, and MuvB (DREAM) that contains mammalian homologs of synMuvB proteins LIN-9, LIN-37, LIN-52, LIN-54, and LIN-53/RBBP4. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3364

Platform:

GPL570

4 Samples

Download data: CEL, CHP

(Submitter supplied) This experiment is a part of global location analysis of the human DREAM complex including subunits: E2F4, RBL2/p130, LIN9 and LIN54. Specifically, the regions in Human Promoter Array 1.0R (GPL5082) bound by: E2F4 in G0-arrested T98G cells E2F4 in S-phase synchronized T98G cells LIN54 in G0-arrested T98G cells LIN54 in S-phase synchronized T98G cells LIN9 in G0-arrested T98G cells LIN9 in S-phase synchronized T98G cells p130 in G0-arrested T98G cells p130 in S-phase synchronized T98G cells were compared with input chromatin. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5082

30 Samples

Download data: BAR, CEL, TXT

Analysis of T98G cells in asynchronously growing state, after 72 hr of serum starvation to induce G0, or after serum restimulation to enter cell cycle. Results provide insight into mammalian cell-cycle gene regulation and mechanisms underlying repression of cell cycle dependent genes in quiescence.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 growth protocol sets

Platform:

GPL570

Series:

GSE8537

4 Samples

Download data: CEL, CHP

(Submitter supplied) The Rb/E2F tumor suppressor regulates gene expression to control the onset and timing of differentiation in many different cell types during development. This critical function makes Rb/E2F a frequent target for inactivation in tumors of diverse tissue origin. However, the mechanisms by which Rb/E2F governs tissue-specific gene regulation in vivo are poorly understood. We have determined the genome-wide binding profiles for components of the C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13776

48 Samples

Download data: BEDGRAPH, GFF3

(Submitter supplied) A temporal gradient of the novel nuclear protein LIN-14 specifies the timing and sequence of stage-specific developmental events in Caenorhabditis elegans. The profound effects of lin-14 mutations on worm development suggest that LIN-14 directly or indirectly regulates stage-specific gene expression. We show that LIN-14 can associate with chromatin in vivo and has in vitro DNA binding activity. A bacterially expressed C-terminal domain of LIN-14 was used to select DNA sequences that contain a putative consensus binding site from a pool of randomized double-stranded oligonucleotides. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL14 GPL2646

6 Samples

Download data

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

Organism:

Caenorhabditis elegans

Type:

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

Platform:

GPL18730

81 Samples

Download data: BW

(Submitter supplied) The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18730

31 Samples

Download data: BW

(Submitter supplied) The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18730

50 Samples

Download data: BW

(Submitter supplied) Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

15 Samples

Download data: CEL

(Submitter supplied) The epidermal-specific ablation of Rb gene leads to increased proliferation, aberrant differentiation, and the disengagement of these processes in vivo and in vitro. These differences in phenotype are more severe with the loss of p107, demonstrating the functional compensation between pRb and p107. As p107 and p130 also exert overlapping functions in epidermis, we have generated Rb(F19/F19)K14cre;Rbl2-/- (pRb-;p130-) mice to analyze possible functional redundancies between pRb and p130. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL339

10 Samples

Download data: CEL

(Submitter supplied) modENCODE_submission_3158 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9309

5 Samples

Download data: BEDGRAPH, GFF3

(Submitter supplied) modENCODE_submission_3157 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9309

9 Samples

Download data: BEDGRAPH, GFF3

(Submitter supplied) modENCODE_submission_2623 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9309

4 Samples

Download data: BEDGRAPH, GFF3

(Submitter supplied) modENCODE_submission_2622 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9309

4 Samples

Download data: BEDGRAPH, GFF3