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TranscriptomicsSMF-ONT S2 clamp RNAi knockdown
Collection of 2 biological replicates of SMF-ONT performed in S2 cell incubated for 72hrs with RNAi targeting Clamp or LacZ (ctrl) transcripts. The footprinting protocol was adapted from Kleinendorst and Barzaghi et al., 2021 and optimised for long-read sequencing and high weight DNA extraction. In...
ORGANISM(S): Drosophila melanogaster 
2026-08-04 | E-MTAB-17018 | biostudies-arrayexpress
GenomicsATAC and Mediator coactivators form a stable complex and regulates a set of non-coding RNA genes
The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embr...
ORGANISM(S): Mus musculus 
2010-06-24 | E-GEOD-21717 | biostudies-arrayexpress
GenomicsSMF-ONT in S2 and OSC Drosophila cell lines
Collection of 2 biological replicates of SMF-ONT performed in S2 and OSC cell lines. The footprinting protocol was adapted from Kleinendorst and Barzaghi et al., 2021 and optimised for long-read sequencing and high weight DNA extraction. In summary, 2.5 million intact nuclei per SMF reaction have be...
ORGANISM(S): Drosophila melanogaster 
2026-08-04 | E-MTAB-14663 | biostudies-arrayexpress
GenomicsIdentification of building principles of methylation states at CG rich regions by high-throughput editing of a mammalian genome
Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of gen...
ORGANISM(S): Mus musculus 
2014-09-30 | E-GEOD-51170 | biostudies-arrayexpress
GenomicsSAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers
Metazoan SAGA and ATAC are distinct multi-subunits complexes that share the same catalytic HAT subunit (GCN5 or PCAF). Here we show that these human HAT complexes are targeted to different genomic loci representing functionally distinct regulatory elements both at broadly expressed and tissue specif...
ORGANISM(S): Homo sapiens 
2011-11-05 | E-GEOD-31052 | biostudies-arrayexpress
GenomicsAmplicon based single molecule footprinting in TC-1 DNMT TKO mESCs after RMCE and after 24h p300 inhibition
To quantify the contribution of specific transcription factor binding versus chromatin context in chromatin opening, we inserted libraries containing hundreds of CREs into a landing pad within a neutral chromatin environment, devoid of activating or repressive chromatin modifications, in mESCs using...
ORGANISM(S): Mus musculus 
2026-05-21 | E-MTAB-16659 | biostudies-arrayexpress
GenomicsAmplicon based single molecule footprinting in TC-1 DNMT TKO mESCs after RMCE - Mutant Libraries
To directly test how individual TFs combine their functions to open chromatin at specific loci, we used synthetic DNA sequences. We generated a library containing all combinations of TF-motif deletions for three CREs: a CTCF-bound region as a positive control (found in \"MutLib1\"), an enhancer with...
ORGANISM(S): Mus musculus 
2026-05-21 | E-MTAB-16657 | biostudies-arrayexpress
GenomicsAmplicon based single molecule footprinting in TC-1 DNMT TKO mESCs after RMCE
To quantify the contribution of specific transcription factor binding versus chromatin context in chromatin opening, we inserted libraries containing hundreds of CREs into a landing pad within a neutral chromatin environment, devoid of activating or repressive chromatin modifications, in mESCs using...
ORGANISM(S): Mus musculus 
2026-05-21 | E-MTAB-16658 | biostudies-arrayexpress
GenomicsChIPseq in 159 DNMT TKO mESCs upon p300 inhibition
To test if H3K27Ac contributes to chromatin accessibility at enhancers, we globally reduced H3K27Ac levels by chemical inhibition of the histone acetylase p300 (with the small molecule A-485, final concentration 3 μM). This dataset includes ChIP-seq data for H3K27Ac with spike-in normalization, comp...
ORGANISM(S): Mus musculus 
2026-06-04 | E-MTAB-14916 | biostudies-arrayexpress
TranscriptomicsBait-capture based single molecule footprinting of Sox2 degron mESC line
Bait-capture based Single Molecule Footprinting (SMF) data. SMF data is obtained by treating extracted nuclei with a GpC and a CpG methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated cytosines as footprints. Data in this ex...
ORGANISM(S): Mus musculus 
2026-01-26 | E-MTAB-15014 | biostudies-arrayexpress
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