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TranscriptomicsiRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data
RNA-seq is a sensitive and accurate technique to compare steady state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we ha...
ORGANISM(S): Homo sapiens 
2015-02-04 | E-GEOD-60462 | biostudies-arrayexpress
GenomicsChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
We used ChIP-Seq to map ERalpha binding sites and to profile changes in RNA polymerase II (RNAPII) occupancy in MCF-7 cells in response to estradiol (E2), tamoxifen or fulvestrant. We identified 10,205 high confidence ERalpha binding sites in response to E2 of which 68% contained an estrogen respons...
ORGANISM(S): Homo sapiens 
2009-03-09 | E-GEOD-14664 | biostudies-arrayexpress
ProteomicsRNAPII interactome via RPB3-FLAG IP
FLAG Ab pull down of chromatin associated proteins in the stable cell line expressing RPB3-3xFLAG (with DOX). Total RNAPII interactome was measured in three conditions; Untreated, 1mM H2O2 treatment for 15 minutes, and 1 hour recovery following media washout.
ORGANISM(S): Homo sapiens (Human) 
2026-06-22 | PXD067831 | Pride
Total rnapii Rpb3 Flag 
GenomicsIntegrator complex regulates NELF-mediated RNA Polymerase II pause/release and processivity at coding genes [ChIP-seq]
RNAPII pausing/termination shortly after initiation is a hallmark of gene regulation. However, the molecular mechanisms involved are still to be uncovered. Here, we show that NELF interacts with Integrator complex subunits (INTScom) forming a stable complex with RNPII and Spt5. The interaction betwe...
ORGANISM(S): Homo sapiens 
2015-05-19 | E-GEOD-60584 | biostudies-arrayexpress
GenomicsGenome-wide profiling of PPAR?:RXR and RNA polymerase II
Genome-wide profiling of PPAR?:RXR and RNA polymerase II reveals temporal activation of distinct metabolic pathways in RXR dimer composition during adipogenesis. Chromatin immunoprecipitation combined with deep sequencing was performed to generate genome-wide maps of peroxisome prolifelator-activat...
ORGANISM(S): Mus musculus 
2008-12-10 | E-GEOD-13511 | biostudies-arrayexpress
TranscriptomicsGenome wide profiling of the RNAPII, γH2AX, H3K4Me1, H3K4M2 and H3K4Me3 in MLL2 F/F and FC/FC MEF cells
We investigated the RNAPII and γH2AX occupancy genome wide by ChIP-Seq in MLL2 F/F and FC/FC80 MEF cells. We found that a week after MLL2 excision (FC/FC cells), a group of genes present higher levels of γH2AX and RNAPII near the TSS, as compared to the control (F/F cells). H3K4Me1, H3K4M2 and H3...
ORGANISM(S): Mus musculus 
2016-04-13 | E-GEOD-73124 | biostudies-arrayexpress
TranscriptomicsExpression data from Saccharomyces cerevisae RNAPII mutant strains
Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. Such genome instability is increased in RNAPII mutants. We performed microarrays to analyze the effect of RNAPII mutations on...
ORGANISM(S): Saccharomyces cerevisiae 
2014-12-04 | E-GEOD-55223 | biostudies-arrayexpress
TranscriptomicsThe C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation
The Carboxy-terminal domain (CTD) of RNA Polymerase II (RNAPII) in mammals undergoes extensive post-translational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the transcriptional co-...
ORGANISM(S): Homo sapiens 
2011-04-01 | E-GEOD-27315 | biostudies-arrayexpress
GenomicsGenome-wide maps of MRE11, NBS1 total RNAPII and phospho-Ser2-RNAPII in WT cells, upon shControl, shMRE11 or shNBS1 treatment, after treatment by DRB and after heat shock in HeLa cells
Genome-wide maps of MRE11, NBS1 total RNAPII and phospho-Ser2-RNAPII in WT cells, upon shControl, shMRE11 or shNBS1 treatment, after treatment by DRB and after heat shock in HeLa cells
PRJNA600988 | ENA
ProteomicsK63-Linked Ubiquitylation of S2P-RNAPII Regulates Transcription in a DNA-PK Inter-Dependent Manner in Response to Double-Strand Breaks
DNA double-strand breaks (DSBs) pose a constant challenge to essential biological functions, including transcription, potentially leading to genomic instability. RNA polymerase II (RNAPII) plays a central role in detecting DNA lesions. Due to difficult-to-repair DSBs, RNAPII removal becomes challeng...
ORGANISM(S): Homo sapiens (Human) 
2026-05-25 | PXD058988 | Pride
Dsbs Ubiquitylation substrates Cul3 Nhej. Ir Ubiquitin ligase 
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