Similar Datasets
Project description:ChIP-seq analysis of NSD2 in IMR-90 cells. We found that NSD2 is enriched at gene bodies of actively transcribed genes and required for maintenace of H3K36me3 levels at these loci.
2020-09-22 | GSE138065 | GEO
Project description:Here we used ChIP-MS to quantitatively profile chromatin-associated proteins that are specifically associated with H3K4me1- and H3K4me3-modified nucleosomes in IMR-90 chromatin.
2023-12-10 | PXD042826 | Pride
Project description:DNA integration is a defining step in the retroviral life cycle and the basis of stable gene transfer in retrovirus-based gene therapy. Previous studies of integration by HIV-based vectors have shown that integration is not random, but favored in active transcription units. Studies to date have focused on HIV integration in dividing cells, leaving open the question of whether integration target site selection might differ in nondividing cells. According to one idea, division of the host cell might be required for favored integration in transcription units, possibly as a result of chromatin remodeling during DNA replication. Here we have investigated this issue by comparing integration in dividing IMR-90 primary lung fibroblasts to integration in nondividing IMR-90 cells arrested in G1 by serum starvation and contact inhibition. We identified several differences in integration site selection in arrested versus dividing cells, including the frequency of integration in transcription units and in gene-rich regions. However, integration in nondividing cells was in fact more favored in transcription units, contrary to the idea that cell division was important for this bias. These data provide the first view of lentiviral integration in nondividing cells and help constrain models for the mechanism of favored integration in genes. Keywords: comparative genomic analysis, dividing versus non-dividing cells.
2005-11-10 | GSE3555 | GEO
Project description:DNA integration is a defining step in the retroviral life cycle and the basis of stable gene transfer in retrovirus-based gene therapy. Previous studies of integration by HIV-based vectors have shown that integration is not random, but favored in active transcription units. Studies to date have focused on HIV integration in dividing cells, leaving open the question of whether integration target site selection might differ in nondividing cells. According to one idea, division of the host cell might be required for favored integration in transcription units, possibly as a result of chromatin remodeling during DNA replication. Here we have investigated this issue by comparing integration in dividing IMR-90 primary lung fibroblasts to integration in nondividing IMR-90 cells arrested in G1 by serum starvation and contact inhibition. We identified several differences in integration site selection in arrested versus dividing cells, including the frequency of integration in transcription units and in gene-rich regions. However, integration in nondividing cells was in fact more favored in transcription units, contrary to the idea that cell division was important for this bias. These data provide the first view of lentiviral integration in nondividing cells and help constrain models for the mechanism of favored integration in genes. Experiment Overall Design: IMR-90 cells (initially passaged 36 times) were cultured in DMEM with 10% FBS until the cells reached 100% confluence, at which point the medium was substituted to contain only 0.5% FBS. The cells were cultivated for 2 weeks prior to harvesting for RNA extraction. 2 arrays were hybridized, using RNA from 2 independent cell cultures. The data of these growth arrested cells was compared to dividing IMR90 cells (Mitchell et al. 2004. PLoS Biology. 2(8):E234).
2008-06-12 | E-GEOD-3555 | biostudies-arrayexpress
Project description:TGFβ is one of most intensively studied regulators of extracellular matrix formation, and has been implicated in the development of pulmonary fibrosis in different models. However, little is know about the role of miRNAs in TGFβ mediated fibrogenic gene regulation. By using miRNA qRT-PCR array, we have identified miRNAs whose expression are regulated by TGFβ in IMR-90 cells. Among those down-regulated miRNAs are miR-29 family members. Knockdown miR-29 in IMR-90 cells results in up-regulation of a large number of extracellular matrix and fibrogenic genes including family members of collagen, laminin, integrin, ADAM and MMP, many of them are predicted or confirmed miR-29 targets. Hierarchichal clustering analysis of mRNA array data revealed that many extracellular matrix and fibrogenic genes up-regulated by TGFβ in IMR-90 cells, are also up-regulated in miR-29 KD cells. Moreover, the similar set of extracellular matrix and fibrogenic genes is also significantly up-regulated in bleomycin treated mouse lungs. Together, our data strongly suggest that downstream of the TGFβ, miR-29 is a master modulator of genes involved in extracellular matrix formation and might play a significant role in pulmonary fibrosis.
2010-03-01 | GSE18651 | GEO
Project description:Genome-wide ChIP-sequencing analysis of PfMCM6 was carried out in trophozoite stage parasites using PfMCM6 antibodies. We have observed that PfMCM6 is highly enriched at the exon regions. Moreover, PfMCM6 was also found in promoter-TSS, transcription termination site (TTS), and intergenic regions in minimal proportion. This study shed some light on PfMCM6 binding sites in Plasmodium falciparum genome.
2023-07-29 | GSE224073 | GEO
Project description:We report genome-wide distribution of Linker histone variant H1t in mouse spermatogenic cells. We found that H1t was mainly located at around transcriptional start site of genic area, positively correlated with the gene expression. This study using ChIP-seq analysis provides genomic distribution of H1t in mouse spermatogenic cells.
2023-03-09 | GSE146733 | GEO
Project description:Genome-wide ChIP-sequencing analysis of PfGCN5 was carried out in asynchronous stage (trophozoite and schizont stage enriched) parasites using PfGCN5 antibodies. We have observed that PfGCN5 is majorly associated with promoter regions of genes. Moreover, a uniform distribution was found in exons, transcription termination site, and intergenic regions. This study shed some light on PfGCN5 binding sites on Plasmodium falciparum genome.
2020-01-01 | GSE142803 | GEO
Project description:In our genetic screen, we found that Ccp1 is an epigenetic stability modulator in centromeres and heterochromatin in S. pombe. In interphase cells,Ccp1-GFP enriched at centromeres. To determine the association sites of Ccp1 with the centromeres and to characterize the global distribution pattern of Ccp1 throughout the genome, ChIP-seq were performed for Myc-tagged Ccp1 (C-terminal fusion protein). The result revealed that Ccp1 associates with the central core regions (cnt and imr) within every single centromere.
2018-06-13 | GSE95046 | GEO