UCL Cancer Institute


Regulatory Genomics Datasets

Omer et al. Cyclin-dependent kinase 9 as a potential target for anti-TNF resistant inflammatory bowel disease. Cell Mol Gastroenterol Hepatol, 2022.
RNA-seq of primary and secondary stimulated CD4+ T cells treated with and without the P-TEFb inhibitor NVP-2 from human colitis and Crohn’s disease patients. 

Tavares et al. JAZF1-SUZ12 dysregulates PRC2 function and gene expression during cell differentiation. Cell Reports, 2022.
ChIP-seq for JAZF1-SUZ12, WT SUZ12 and SUZ12D93 in mouse ES cells, ChIP-seq for H3K27me3 and H4Kac in ES cells expressing these proteins, RNA-seq of primary human endometrial stromal cells (hEnSC) expressing these proteins, ChIP-seq for H3K27me3 in hEnSC. 

Hertweck et al. The Th1 cell lineage-determining transcription factor T-bet suppresses Th2 gene expression by redistributing GATA3 away from Th2 genes. Nucleic Acids Research, 2022.
ChIP-seq for T-bet, GATA3 and H3K27ac in mouse EL4 cells expressing either factor or both factors together. RNA-seq in the same cell lines. ATAC-seq in EL4 cells with and without T-bet.

Lo et al. A population of CD4+ T cells with a naïve phenotype stably polarized to the Th1 lineage. European Journal of Immunology, 2022.
RNA-seq of YFP+ (T-bet-experienced) and YFP- (T-bet inexperienced) naïve-like and memory CD4+ T cells. 

Skalska et al. Nascent RNA antagonises the interaction of a set of regulatory proteins with chromatin, Mol Cell, 2022.
Mass spec of the chromatin fraction after RNA pol II inhibition with triptolide and flavopiridol and mass spec of nucleosome binding proteins in nuclear extract with and without RNA degradation by treatment with RNaseA in mouse ES cells. PRIDE datalink
Mass spec of the chromatin fraction after RNA depletion by treatment with RNaseA. PRIDE datalink
RNA-seq of mouse ES cell whole cell extract and chromatin-associated polyA+ and total RNA and iCLIP for P-TEFb and LARP6. GEO datalink.

Cottone et al. Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death, Cancer Research, 2020.
ChIP-seq for H3K27me3, H3K27ac, H3K4me3 and H3K9me3 and RNA-seq in chordoma cells treated with KDM6A/6B inhibitors.

Śledzińska et al. Regulatory T cells restrain IL-2- and Blimp-1-dependent acquisition of cytotoxic function by CD4+ T cells, Immunity, 2020.
Microarray data for CD4+ T cells from mouse tumours and lymph nodes.

Beltran et al. G-tract RNA removes Polycomb Repressive Complex 2 from genes, Nature Stuctural and Molecular Biology, 2019.
iCLIP for SUZ12, FUS and HNRNPC input samples in mouse ESC.

Anandagoda et al. microRNA-142-mediated repression of phosphodiesterase 3B critically regulates peripheral immune tolerance, Journal of Clinical Investigation, 2019.
ChIP-seq for Foxp3 in murine Th1 and iTreg cells.

Soderquest et al. Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease. PLOS Genetics, 2017.
ChIP-seq for T-bet in individuals heterozygous for inflammatory disease-associated genetic variants. Datalink

Hertweck et al. T-bet Activates Th1 Genes through Mediator and the Super Elongation Complex. Cell Reports, 2016.
ChIP-seq for RNA pol II, P-TEFb and H3K4me3 in human Th1 and Th2 cells,  T-bet, Med1, Aff4, Brd4 and RelA in human Th1 cells, P-TEFb, Med1, Aff4, Brd4 and RelA in mouse WT and T-bet-/- Th1 cells, T-bet, P-TEFb, Med1, Aff4, Brd4 and RelA in EL4 cells with and without T-bet, RNA-seq in human Th1 and Th2 cells.

Beltran et al. The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Research, 2016.
iCLIP for PRC2, FUS and HnRNP C, RNA-seq in WT and Ezh2-/- mouse ES cells, ChIP-seq for Ezh2 and Suz12 in WT and Ezh2-/- ES cells, ChIP-seq for SUZ12 and p300 in ES cells with and without RNase A treatment.

Gunnell et al. RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth. Nucleic Acids Research, 2016.
ChIP-seq for EBV EBNA2 in lymphoblastoid cells.

Ramasubramanyan et al. Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression. Nucleic Acids Research, 2015.
RNA-seq of B cells with and without EBV Zta expression.

Vlachogiannis et al. The Dnmt3L ADD Domain Controls Cytosine Methylation Establishment during Spermatogenesis. Cell Reports, 2015.
MethylC-Seq of wild-type and Dnmt3LA/A 1dpp prospermatagonia.

Bouwman et al. Human immunodeficiency virus Tat associates with a specific set of cellular RNAs. Retrovirology, 2014.
Microarray analysis of HIV Tat and Ago2 RNA IP and gene expression microarray analysis of T cell lines expressing HIV Tat and of primary T cells infected with HIV. Datalink

Gokmen et al. Genome-Wide Regulatory Analysis Reveals T-bet Controls Th17 Lineage Differentiation through Direct Suppression of IRF4. J Immunol. 2013.
ChIP-Seq of T-bet in mouse WT and Tbx21-/- Th1 cells  

McClellan et al. Modulation of enhancer looping and differential gene targeting by epstein-barr virus transcription factors directs cellular reprogramming. PLoS Pathogens 2013.
ChIP-Seq of EBV EBNA2 and EBNA3 in the MutuIII Burkitt’s lymphoma line 

Kanhere et al. T-bet and GATA3 orchestrate Th1 and Th2 cell differentiation through lineage-specific targeting of distal regulatory elements. Nature Communications 2012.
ChIP-Seq of T-bet and GATA3 in human Th1 and Th2 cells Gene expression microarray analysis of Thp, Th1 and Th2 cells from WT, Tbx21-/- and Gata-3 fl/fl x Tnfrsf4-Cre mice 

Kanhere et al. Short RNAs are transcribed from repressed Polycomb target genes and interact with Polycomb Repressive Complex-2. Mol Cell 2010.
Gene expression microarray analysis of short ncRNAs in human T cells ChIP-Chip of histone modifications and RNA Pol II in human T cells 

Jenner et al., The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes. Proc. Natl. Acad. Sci. USA 2009.
ChIP-Chip of T-bet and GATA3 in human Th1 and Th2 cells. Gene expression microarrays analysis of human Th1 and Th2 cells, and in murine Tbx21-/- /Ifng-/- T cells transduced with T-bet-RV or GFP-RV