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TranscriptomicsAtypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana
In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many pr...
ORGANISM(S): Arabidopsis thaliana 
2012-11-22 | E-GEOD-34207 | biostudies-arrayexpress
ProteomicsWidespread hydroxylation of unstructured lysine-rich protein domains by JMJD6
The Jumonji domaining-containing protein JMJD6 is a 2-oxoglutarate dependent dioxygenase that has been implicated in a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing and co-transcriptional processing. Al...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2022-08-02 | PXD031221 | Pride
Human Lc-msms Hydroxylation Jmjd6 Lysine derivatisation 
ProteomicsJMJD6 interactome screen from "Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6"
The Jumonji domaining-containing protein JMJD6 is a 2-oxoglutarate dependent dioxygenase that has been implicated in a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing and co-transcriptional processing. Al...
ORGANISM(S): Homo sapiens (Human) 
2022-08-02 | PXD031155 | Pride
Lc-msms Dia Human Hela Interactome Orbitrap fusion lumos Jmjd6 
ProteomicsMITOMICS: defining mitochondrial protein functions through deep multi-omic profiling
Mitochondria are epicenters of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles and have linked their dysfunction to over 150 distinct disorders. However, hundreds of mitochondrial proteins still lack clea...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-01-11 | MSV000086685 | MassIVE
ProteomicsProteomic analysis of experimental foodcrusts reveals discrepancies between food input and recovered protein signal
In order to investigate how representative the recoverable proteins from charred organic residues (foodcrust) are of the food mixture cooked to produce them, a protein-rich (salmon), lipid-rich (beef fat) and carbohydrate-rich (beetroot) food were mixed, cooked and analysed. The three ingredients we...
ORGANISM(S): Bos taurus (Bovine) Salmo salar (Atlantic salmon) blank sample Beta vulgaris (Sugar beet) 
2025-08-25 | PXD059930 | Pride
Organic residue Experimental archaeology Foodcrust Complex mixtures Metaproteomics 
GenomicsA SNF2 protein targets variable copy number repeats and thereby influences allele-specific expression
ATRX is an X-linked gene of the SWI/SNF family whose role in vivo is currently unknown. Mutations in ATRX cause syndromal mental retardation. ATRX binds to tandem repeat (TR) sequences both in heterochromatin (e.g. telomeres) and euchromatin. Genes associated with these TRs can be dysregulated when ...
ORGANISM(S): Homo sapiens 
2010-11-02 | E-GEOD-22162 | biostudies-arrayexpress
ProteomicsDirect evidence of milk consumption from ancient human dental calculus, St Helena
This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-07-20 | MSV000079939 | MassIVE
ProteomicsDirect evidence of milk consumption from ancient human dental calculus, northern southwest Asia
This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-08-18 | MSV000080064 | MassIVE
TranscriptomicsTranscription profiling of Arabidopsis mutant REVOLUTA (HDZIPIII) to identify downstream targets
The establishment of ad/abaxial polarity is a fundamental event in plant development. It is critical for correct polar development of the leaf (the upper portion of the leaf is chloroplast rich and optimized for light capture while the lower portion is optimized for gas exchange) and for creating a...
ORGANISM(S): Arabidopsis thaliana 
2008-06-15 | E-GEOD-7003 | biostudies-arrayexpress
TranscriptomicsSharkey trophoblast
Transcriptional profiling comparison of human primary villous trophoblast and extra-villous trophoblast (VT and EVT respectively) cells, isolated from the placenta at 8 to 12 weeks gestation, with complimentary transcriptional profiling of choriocarcinoma cell lines JEG-3 and JAR. Based on phenotypi...
ORGANISM(S): Homo sapiens 
2011-04-28 | E-MTAB-429 | biostudies-arrayexpress
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