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Transcriptomics4C-seq of a K562 cell line model with a patient-based t(3;8) translocation
Chromosome Conformation Capture Sequencing (4C-seq) was performed to assess interaction between the MYC super-enhancer and the EVI1 promoter under different conditions. Sample preparation was performed as previously described (van de Werken et al., 2012). In short, genomic regions that are spatially...
ORGANISM(S): Homo sapiens 
2021-07-26 | E-MTAB-9958 | biostudies-arrayexpress
GenomicsMaternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus [Bisulfite-Seq]
Maternal 5-HT1A-receptor (R) is required for the timely development of the hippocampus and the establishment of emotional behaviors in Swiss-Webster (SW) mice. A partial and/or complete loss of maternal 5-HT1AR results in delayed ventral dentate granule cell (v-DGC) development and subsequent anxie...
ORGANISM(S): Mus musculus 
2013-02-04 | E-GEOD-35854 | biostudies-arrayexpress
GenomicsChIP-seq for the identification of enhancer and super enhancers in Acute Myeloid Leukemia cells with a 3q-aberration
To infer enhancers and super enhancers in Acute Myeloid Leukemia (AML) Cell lines with a 3q-aberration we determined regions enriched for H3K27AC, H3K4ME3, H3K4ME1, P300, and BRD4 in MOLM1. Additionally we determined regions enriched for P300 and BRD4 in the cell line Mutz3 which also harbors a 3q-a...
ORGANISM(S): Homo sapiens 
2014-04-03 | E-MTAB-2224 | biostudies-arrayexpress
TranscriptomicsAmplicon-seq of an enhancer region targeted by CRISPR to assess the mutations introduced by different sgRNA guides
Following a CRISPR enhancer scan covering the GATA2 super-enhancer region, the top sgRNAs were selected for further inspection. MUTZ3 cells were thus treated with the selected sgRNAs and the region of interested was subjected to amplicons sequencing (amplicon-seq). To that end, we used the Illumina ...
ORGANISM(S): Homo sapiens 
2021-07-26 | E-MTAB-9945 | biostudies-arrayexpress
TranscriptomicsGenome-wide DNA methylation profiling of Acute Myeloid Leukemia
We hypothesized that DNA methylation distributes into specific patterns in cancer cells, which reflect critical biological differences. We therefore examined the methylation profiles of 344 patients with acute myeloid leukemia (AML). Clustering of these patients by methylation data segregated patien...
ORGANISM(S): Homo sapiens 
2010-01-12 | E-GEOD-18700 | biostudies-arrayexpress
UnknownIdentification of a 24-gene prognostic signature that improves the European LeukemiaNet risk classification of acute myeloid leukemia: an international collaborative study.
Not available
S-EPMC3595425 | biostudies-literature
TranscriptomicsGenome-wide DNA methylation in CEBPA mutant and CEBPA silenced AML
Acute Myeloid Leukemia (AML) is a heterogeneous disease from the molecular and biological standpoints, and even patients with a specific gene expression profile may present clinical and molecular heterogeneity. We studied the epigenetic profiles of a cohort of patients that shared a common gene expr...
ORGANISM(S): Homo sapiens 
2010-05-07 | E-GEOD-14417 | biostudies-arrayexpress
GenomicsAmplicon sequencing of a K562 cell line model with a patient-based t(3;8) translocation following CRISPR treatment
Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequenci...
ORGANISM(S): Homo sapiens 
2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress
GenomicsChIP-seq of a K562 cell line model with a patient-based t(3;8) translocation
ChIP-seq was performed to assess changes in the activity of the MYC SE upon deletion of its modules or CTCF binding sites. Immunoprecipitation of crosslinked chromatin was performed with antibodies directed against H3K27Ac (Diagenode C15410196), H3K9Ac (Diagenode C15410004), H3K4me3 (Diagenode C1541...
ORGANISM(S): Homo sapiens 
2021-07-26 | E-MTAB-9965 | biostudies-arrayexpress
TranscriptomicsCCAAT/enhancer-binding protein alpha target genes in myeloid progenitor cells uncovered by chromatin IP
CCAAT/enhancer-binding protein alpha (C/EBPM-NM-1) is a lineage-specific transcription factor that directs development of granulocytes. To obtain insights into the genome-wide transcriptome of wild type C/EBPM-NM-1, we have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-ch...
ORGANISM(S): Mus musculus 
2013-12-01 | E-GEOD-19321 | biostudies-arrayexpress
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