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no omics definedTranscription profiling of human cell lines and tissues - Luscombe re-analysis of GNF/Novartis data
The expression data utilized in this analysis derives from the raw data published by Su et al. 2004 (also known as GNF/Novartis dataset or E-AFMX-5 in ArrayExpress, GSE1133 and GDS596 in GEO). The data contains 79 different human tissues and cell types with 2 replicates per tissue/cell type. The dat...
ORGANISM(S): Homo sapiens 
2008-02-23 | E-TABM-145 | biostudies-arrayexpress
ProteomicsCharacterization of chromatin associated RNA-binding proteins by SPACE
Chromatin processes such as DNA replication, transcription and RNA processing are mediated by intermolecular transactions among proteins, RNAs and the genome. Although DNA-protein and RNA-protein interactions have been studied extensively, reliable and efficient identification of chromatin-associate...
ORGANISM(S): Mus musculus (Mouse) 
2021-11-25 | PXD023903 | Pride
Proteomics Pluripotency Idr Chromatin Dazl Rbp 
TranscriptomicsTranscriptome-wide mapping of hnRNP C and U2AF65 using iCLIP
iCLIP experiment to assess the binding of the highly abundant nuclear RNA-binding protein hnRNP C and core splicing factor U2AF65 on a genomic scale. To investigate how both proteins compete for binding at a subset of sites, U2AF65 iCLIP experiments were performed from both HNRNPC knockdown and cont...
ORGANISM(S): Homo sapiens 
2013-01-31 | E-MTAB-1371 | biostudies-arrayexpress
TranscriptomicsMNase-Seq of isolated mono-nucleosomes from strains W303 (wild-type) and htz1∆.
Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mono-nucleosomes harbo...
ORGANISM(S): Saccharomyces cerevisiae S288c 
2019-05-08 | E-MTAB-7926 | biostudies-arrayexpress
GenomicsChIP-seq of RNA polymerase II using pan-pol II and S2-phosphorylated C-terminal domain antibodies in mouse embryonic stem cells
Our proteomics data (PXD030253) indicate RNA polymerase II is co-localized with Aldh18a1. To confirm this observation using an orthogonal method we performed ChIP-seq experiments to identify the binding patterns of RNA polymerase II in general, and RNA polymerase II with S2-phosphorylated CTD. We al...
ORGANISM(S): Mus musculus 
2022-06-01 | E-MTAB-11510 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA-seq of the 16-cell stage Ciona embryo
Ciona develops according to a stereotyped or invariant lineage. This allowed us to collect precisely defined replicates of all eight blastomeres of the right half of the embryo at the 16-cell stage of Ciona. We manually dissected each embryo, collecting and identifying each cell before library prepa...
ORGANISM(S): Ciona robusta 
2020-03-06 | E-MTAB-6117 | biostudies-arrayexpress
TranscriptomicsATAC-seq on ESCs undergoing directed differentiation towards defined neural fates
We have used ATAC-seq to track cell state changes that occur during the differentiation of mouse embryonic stem cells to defined neural progenitor fates. We have performed ATAC-seq every 24 hours in cells en route to 3 distinct neural progenitors fates, anterior, hindbrain and spinal cord. This has ...
ORGANISM(S): Mus musculus 
2018-08-27 | E-MTAB-6337 | biostudies-arrayexpress
Transcriptomicsmonitoring splicing changes in TIA1/TIAL1 double knockdown vs control HeLa cells
Not available
ORGANISM(S): Homo sapiens 
2010-10-26 | E-MTAB-526 | biostudies-arrayexpress
GenomicsSox2 ChIP-seq in hindbrain and spinal cord neural progenitors differentiated from mouse embryonic stem cells
Sox2 is a key determinant of neural cell identity, expressed in neural progenitors from anterior to posterior levels. We asked if the occupancy of this factor changes in neural progenitors with different axial identities. To this end, we performed the directed differentiation of mouse embryonic stem...
ORGANISM(S): Mus musculus 
2018-08-27 | E-MTAB-6348 | biostudies-arrayexpress
TranscriptomicsCut&Run of Aldh18a1 using 46C mouse ES cells
Using a proteomic approach we identified Aldh18a1 as a protein co-localized with RNA polymerase II. We then carried out Aldh18a1 Cut&Run assays to confirm its co-localization with RNA polymerase II (E-MTAB-11510). As a result, we observed Aldh18a1 is co-localized with RNA polymerase II primarily on ...
ORGANISM(S): Mus musculus 
2022-06-01 | E-MTAB-11513 | biostudies-arrayexpress
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