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TranscriptomicsA transcriptome-wide atlas of RNP compositions reveals diverse classes of mRNAs and lncRNAs
Aim: To determine how different classes of transcript (e.g. lncRNAs and mRNAs) are defined in the cell. Approach: We determined the transcriptome-wide targets of key RNA packaging, maturation, export and turnover factors. We used the CRAC technique, whereby RNA:protein interactions are fixed by UV ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-08-29 | E-GEOD-46742 | biostudies-arrayexpress
TranscriptomicsRole of NFBD1 in global gene expression
NFBD1 (nuclear factor with BRCT domains 1), also known as MDC1 (mediator of DNA damage signaling 1), is a protein involved in the ATM signaling pathway in response to DNA damage. In addition to a role in signaling, NFBD1 possesses transactivation activity, suggesting that it may influence transcrip...
ORGANISM(S): Homo sapiens 
2011-06-16 | E-GEOD-23010 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae
Purpose: The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. We applied an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between individu...
ORGANISM(S): Saccharomyces cerevisiae 
2012-09-25 | E-GEOD-40046 | biostudies-arrayexpress
Transcriptomics21T series cell lines show distinct stage-specific gene expression alterations
Pathologic and epidemiologic evidence has led to a histologic model of breast cancer progression that involves advancement through specific morphologic stages including atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive mammary carcinoma (IMC), although not necessarily a...
ORGANISM(S): Homo sapiens 
2010-04-06 | E-GEOD-18370 | biostudies-arrayexpress
TranscriptomicsTCF7 is a key regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line
A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hema...
ORGANISM(S): Mus musculus 
2012-03-29 | E-GEOD-30068 | biostudies-arrayexpress
TranscriptomicsLoss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough
Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise ...
ORGANISM(S): Saccharomyces cerevisiae S288c 
2015-12-02 | E-MTAB-3642 | biostudies-arrayexpress
TranscriptomicsRNA sequencing of two protein phosphatases(ppm2 and ppm5) knockouts in Plasmodium berghei to study their role in the parasite's sexual development
To identify protein phosphatases (PP) that are essential during asexual blood stage development in Plasmodium berghei, we attempted systematic deletion of the 30 P. berghei PP genes using double homologous recombination. Of these, we performed strand-specific RNA-sequencing (RNA-Seq) analysis for 2...
ORGANISM(S): Plasmodium berghei 
2014-04-16 | E-MTAB-2215 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse hematopoietic cells at different differentiation stages: hematopoietic stem cells (HSCs), progenitor cells (HPCs), and granulocytes somatic cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer
Since the creation of Dolly, the first sheep cloned via somatic cell nuclear transfer (SCNT), in 1997, more than a dozen species of mammals have been cloned using this technology. One hypothesis for the limited success of cloning via SCNT (1-5%) is that the clones are likely derived from adult stem...
ORGANISM(S): Mus musculus 
2008-06-14 | E-GEOD-5677 | biostudies-arrayexpress
TranscriptomicsIRF4, a master transcription factor, regulates genes involved in BCR signaling, antigen processing and presentation, and GC development [expression array]
Interferon regulatory factor 4 (IRF4) is a master transcription factor required for the maturation of germinal center B cells that eventually develop into antibody secreting plasma cells and memory B cells. IRF4-deficient mice exhibit a profound reduction in serum immunoglobulin levels. In spite of...
ORGANISM(S): Homo sapiens 
2015-12-15 | E-GEOD-64269 | biostudies-arrayexpress
TranscriptomicsGBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome)
Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic a...
ORGANISM(S): Homo sapiens 
2026-09-12 | E-MTAB-17183 | biostudies-arrayexpress
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