Similar Datasets
Project description:These are three biological replicates. HeLa cells were crosslinked on separate days. In each case, a matched total from the same crosslinking was produced in parallel. Amplicons were made from each and hybridized onto ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Goal was determination of E2F1 binding sites in HeLa cells by using ChIP-chip methodology. See Farnham Lab website for downloadable protocol for ChIP or supplementary file (Chip_protocol.txt) below. NimbleGen performed all array processing. See NimbleGen website for information on array procedures.
2010-07-01 | E-GEOD-4306 | biostudies-arrayexpress
Project description:These are three biological replicates. HeLa cells were crosslinked on separate days. In each case, a matched total from the same crosslinking was produced in parallel. Amplicons were made from each and hybridized onto ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Keywords: ChIP-chip
2006-02-28 | GSE4306 | GEO
Project description:Control IgG ChIP vs matched total for HeLa cells. Three biological replicates. Keywords: ChIP-chip
2006-03-09 | GSE4338 | GEO
Project description:Control IgG ChIP vs matched total for HeLa cells. Three biological replicates. ChIP-chip of IgG; look for non-specific binding sites.
2010-07-01 | E-GEOD-4338 | biostudies-arrayexpress
Project description:STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). The chromatin-immunoprecipitation protocol is the same for all samples, however the labelling and hybridization protocols differ between Nimblegen and custom maskless arrays. Keywords = Transcription Factor Binding, STAT1, ChIP-chip, Human, Genome Tiling Arrays Keywords: other
2005-05-27 | GSE2714 | GEO
Project description:To have a global picture of the miRNAs dependent on the transcription factor E2F1, we assessed small RNA changes, by RNA-sequencing, of HeLa cells transfected with an siRNA targeting E2F1 or a control siRNA.
2021-04-12 | GSE147361 | GEO
Project description:E2F transcription factors are known regulators of the cell cycle, proliferation, apoptosis and differentiation. We reveal an essential role for E2F1 in liver through the regulation of glycolysis and lipogenesis. E2F1 deficiency leads to a decreased in glycolysis and de novo synthesis of fatty acids in hepatocytes. ChIP-Seq was performed to determine direct tagets of E2F1 in hepatocytes. We highlight that E2F1 directly binds the promoters of genes implicated in metabolic process and notably key lipogenic genes to control these pathways.
2015-12-01 | GSE74006 | GEO
Project description:Total RNA samples from three biological replicates in which the hsa-mir-98 was overexpressed in HeLa cells were profiled by gene expression. As negative control, we used total RNA samples from HeLa cells transfected with cel-mir-67 Keywords: gene expression array-based (RNA / in situ oligonucleotide)
2008-12-17 | GSE12092 | GEO
Project description:Total RNA samples from three biological replicates in which the hsa-mir-26b was overexpressed in HeLa cells were profiled by gene expression. As negative control, we used total RNA samples from HeLa cells transfected with cel-mir-67 Keywords: gene expression array-based (RNA / in situ oligonucleotide)
2008-12-17 | GSE12091 | GEO
Project description:Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and mutant E2F1 proteins. First, we performed ChIP-seq for tagged wt E2F1. Then, we analyzed E2F1 proteins that lacked the N terminal SP1 and cyclin A binding domains, the C terminal transactivation and pocket protein binding domains, and the internal marked box domain. Surprisingly, we found that the ChIP-seq patterns of the mutant proteins were identical to that of wt E2F1. However, mutation of the DNA binding domain abrogated all E2F1 binding to the genome. These results suggested that the interaction between the E2F1 DNA binding domain and a consensus motif may be the primary determinant of E2F1 recruitment. To address this possibility, we analyzed the in vivo binding sites for the in vitro-derived consensus E2F1 motif (TTTSSCGC) and also performed de novo motif analysis. We found that only 12% of the ChIP-seq peaks contained the TTTSSCGC motif. De novo motif analysis indicated that most of the in vivo sites lacked the 5M-CM-"M-BM-^@M-BM-^Y half of the in vitro derived consensus, having instead the in vivo consensus of CGCGC. In summary, our findings do not provide support for the model that protein-protein interactions are involved in recruiting E2F1 to the genome, but rather suggest that recognition of a motif found at most human promoters is the critical determinant. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 9 total ChIP-seq datasets; four different HA-ER-E2F1 mutants, and one HA ER E2F1 wild type dataset done in duplicate, from 5 different stable cell lines derived from MCF7 cells; Three Input replicates from 2 different stable cell lines derived from MCF7 cells; HA ER E2F1 wild type duplicate dataset from MCF7 stable cells; 1 HA ER E2F1 DBDmut replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TC replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TN/C replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TMB replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TMB replicate from MCF7 stable cells cells, 3 Input replicates from MCF7 stable cells cells.
2011-04-04 | E-GEOD-28286 | biostudies-arrayexpress