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ProteomicsA comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans
DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to define the landscape of D...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2023-09-12 | PXD045311 | Pride
Adductomics Strp mrm 
TranscriptomicsSingle cell RNA-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control
This study used scRNA-seq to characterise the transcriptome in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using ...
ORGANISM(S): Homo sapiens 
2023-04-30 | E-MTAB-11138 | biostudies-arrayexpress
ProteomicsTumour mtDNA mutations drive aerobic glycolysis to enhance checkpoint blockade (part 2)
Mitochondrial DNA (mtDNA) encodes essential machinery for respiration and metabolic homeostasis but is paradoxically among the most common targets of somatic mutations in the cancer genome, with truncating mutations in complex I genes being over-represented1 . While mtDNA mutations have been associ...
ORGANISM(S): Mus musculus (Mouse) 
2023-11-08 | PXD044987 | Pride
Melanoma Cancer Complex i Mitochondrial dna 
TranscriptomicsSingle cell ATAC-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control
This study used snATAC-seq to profile Chromatin accessibility in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated usin...
ORGANISM(S): Homo sapiens 
2023-04-30 | E-MTAB-11139 | biostudies-arrayexpress
TranscriptomicsSingle cell RNA-seq of hiPSC-derived kidney organoids differentiated within self-assembling peptide hydrogels and the animal-derived matrix Matrigel
scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respectiv...
ORGANISM(S): Homo sapiens 
2022-10-31 | E-MTAB-11149 | biostudies-arrayexpress
TranscriptomicsImmune cells direct epithelial maturation during early human lung development
The adult human lung harbours a significant proportion of immune cells, which are known to play a crucial role in both normal lung homeostasis and pathogenesis. In this work, we collected CD45-enriched human lung cells from 6 to 22 week post conception (pcw) and built a single-cell transcriptome and...
ORGANISM(S): Homo sapiens 
2022-12-09 | E-MTAB-11528 | biostudies-arrayexpress
TranscriptomicsA gp130-induced Src/Yes-YAP Cascade Links Inflammation to Regeneration in the Mammalian Intestine
gp130Act cDNA was PCR-amplified and inserted into a plasmid containing the 12.4-kb Villin promoter. The 15.7-kb expression cassette was excised by PmeI digestion, purified, and injected into fertilized C57BL/6 oocytes to obtain founder mice, two of which transmitted the gp130Act transgene. Small int...
ORGANISM(S): Mus musculus 
2015-02-21 | E-MTAB-2400 | biostudies-arrayexpress
TranscriptomicsEnterococcus faecalis OG1RF control vs. treatment with ampicillin, bacitracin, cephalothin, or vancomycin
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Enterococcus faecalis OG1RF 
2013-03-19 | E-GEOD-45306 | biostudies-arrayexpress
TranscriptomicsStreptococcus mutans UA159 vs. spx mutant strains
Transcriptional profiling to investigate the regulatory roles of SpxA and SpxB of S. mutans. RNA was extracted from four replicate samples of each strain of interest (spxA mutant, spxB mutant, spxAB double-mutant, UA159 wild type) and labeled with Cy3. For each replicate, labeled RNA was hybridized...
ORGANISM(S): Streptococcus mutans 
2010-05-16 | E-GEOD-19656 | biostudies-arrayexpress
TranscriptomicsStreptococcus mutans UA159 vs. clp mutant strains
Transcriptional profiling to investigate the roles of ClpP and ClpX of S. mutans RNA was extracted from four replicate samples of each strain of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA15...
ORGANISM(S): Streptococcus mutans 
2011-06-10 | E-GEOD-29871 | biostudies-arrayexpress
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