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Transcriptomics4f-SAMMY-seq (Sequential Analysis of MacroMolecules Accessibility) and total RNA-seq data from prostate biopsies of 25 chemo-naïve patients (7 healthy biopsies and 18 tumor biopsies)
We used a groundbreaking epigenomic profiling technique developed in our laboratory, the 4f-SAMMY-seq, along with RNA-seq on 7 healthy biopsies and 18 prostate tumor biopsies. Our study represents the first direct examination of chromatin organization in patient-derived prostate biopsies. Leveraging...
ORGANISM(S): Homo sapiens 
2025-08-21 | E-MTAB-14226 | biostudies-arrayexpress
TranscriptomicsscRNA-seq (Smart-seq3xpress) of a human and mouse cell line mix (4T1, Jurkat, MCF-7, MDA-MB-231, THP-1) labeled with synthetic RNA barcodes
Showcasing the use and recovery of synthetic RNA-based barcodes for sample multiplexing. Cell lines were suspended and individually labeled before pooling, sorting, and Smart-seq3xpress scRNA-seq library generation.
ORGANISM(S): mixed sample 
2026-10-09 | E-MTAB-17623 | biostudies-arrayexpress
TranscriptomicsBait-capture based single molecule footprinting 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 bait capture single molecule footprinting (SMF) data, compa...
ORGANISM(S): Mus musculus 
2026-07-29 | E-MTAB-17191 | biostudies-arrayexpress
TranscriptomicsSTAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescence
Heart failure with preserved ejection fraction (HFpEF) accounts for half of heart failure cases and is characterised by reduced pericyte coverage. While the contributions of other cardiac cell types to HFpEF are well-studied, the role of pericytes remains less understood. Using murine single-nucleus...
ORGANISM(S): Homo sapiens 
2025-04-25 | E-MTAB-15019 | 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
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
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
TranscriptomicsscRNA-seq (3' droplet) of a human and mouse cell line mix (MCF-7, MPC, IMR-5, MDA-MB-231, A549, 4T1, HEK-293, B16, THP-1) labeled with synthetic RNA barcodes
Showcasing the use of synthetic RNA-based barcodes for sample multiplexing in droplet-scRNA-seq. Cell lines were suspended and individually labeled before pooling and 3' droplet scRNA-seq library generation.
ORGANISM(S): mixed sample 
2026-10-09 | E-MTAB-17624 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of organoids derived from fetal uterine epithelial primary samples
We tested the impact of BPA and benzyl butyl phthalate (BBP), a representative phthalate ester, on fetal uterine epithelial organoids derived from 12 and 17 PCW samples.
ORGANISM(S): Homo sapiens 
2025-08-05 | E-MTAB-15457 | biostudies-arrayexpress
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