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ProteomicsQuantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies
Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes glo...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-10-21 | MSV000090570 | MassIVE
ProteomicsQuantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies
Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes glo...
ORGANISM(S): Homo sapiens (Human) 
2021-05-06 | PXD020586 | Pride
Tmtpro Lc-ms Single cell proteomics Scms 
GenomicsInitiation of MLL-rearranged AML is orchestrated by C/EBPa
Acute Myeloid Leukemia (AML) is associated with a number of genetic and epigenetic events that result in malignant transformation of hematopoietic cells. In particular, transcription factors essential for normal hematopoiesis and stem cell function are often found mutated leading to the formation of...
ORGANISM(S): Mus musculus 
2013-12-10 | E-GEOD-47003 | biostudies-arrayexpress
GenomicsTemporal mapping of C/EBPα and –β binding during liver regeneration
Temporal mapping of C/EBPα and –β binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Timeseries ChIP-seq of transcription factors C/EBPα and –β, and Pol II in time points 0, 3, 8, 16, 24, 36, 48, 168 hours after pa...
ORGANISM(S): Mus musculus 
2013-01-24 | E-GEOD-42321 | biostudies-arrayexpress
GenomicsAmplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq
ChIP-seq is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low cell numbers. We describe a robust, simple and scalable methodology for Ch...
ORGANISM(S): Mus musculus 
2015-02-01 | E-GEOD-55850 | biostudies-arrayexpress
TranscriptomicsIntegrative analysis of histone ChIP-seq and gene expression microarray data using Bayesian mixture models
Histone modifications are a key epigenetic mechanism to activate or repress the expression of genes. Data sets of matched microarray expression data and histone modification data measured by ChIP-seq exist, but methods for integrative analysis of both data types are still rare. Here, we present a no...
ORGANISM(S): Mus musculus 
2014-02-05 | E-GEOD-49975 | biostudies-arrayexpress
TranscriptomicsDevelopment of MLL-rearranged leukemia is dependent on a transcriptional program orchestradt by C/EBPα
Translocations involving the MLL genes are frequently found in Acute Myeloid Leukemia (AML) and are associated with poor prognosis. The MLL fusion proteins act as aberrant transcription factor activating a transcriptional program that transforms the cells, potentially through collaboration with othe...
ORGANISM(S): Mus musculus 
2013-12-10 | E-GEOD-46534 | biostudies-arrayexpress
TranscriptomicsDeletion of Cebpa from HSCs
In this study, we use a conditional mouse model for Cebpa to investigate the significance of C/EBPα in HSCs. The frequency of HSCs is unaltered following deletion of C/EBPα, however, upon serial transplantations of either full BM or purified HSCs, the stem cells and stem cell activity is lost. This ...
ORGANISM(S): Mus musculus 
2013-12-10 | E-GEOD-42498 | biostudies-arrayexpress
TranscriptomicsLoss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis [Agilent]
DNA methylation is tightly regulated throughout mammalian development and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested to protect...
ORGANISM(S): Mus musculus 
2015-04-30 | E-GEOD-68415 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide study of alternative splicing in nonsense-mediated mRNA decay-deficient mouse tissues
A major task in analyzing alternative splicing (AS) by RNA-Seq is to explore and quantify the differential representation of various splice classes and the protein-coding potential of the mapped reads. To this end, we have generated a streamlined bioinformatic pipeline available to the scientific co...
ORGANISM(S): Mus musculus 
2012-05-01 | E-GEOD-26561 | biostudies-arrayexpress
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