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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
TranscriptomicsSingle-Cell Multi-omics RNA and ATAC Sequencing of In Vitro Hematoendothelial Differentiation from Mouse Embryonic Stem Cells
An in vitro differentiation system using mouse embryonic stem cells to capture multiple differentiation timepoints: days 3, 4, 5, 6, and 7 as scMultiome (ATAC+RNA) and days 0, 2, and 4 as scRNA-seq. scMultiome libraries were generated using the Single Cell Multiome ATAC + Gene Expression v1 chemistr...
ORGANISM(S): Mus musculus 
2025-12-11 | E-MTAB-16347 | biostudies-arrayexpress
TranscriptomicsRNA sequencing comparing the effect of the introduction of CSF3R-d715 in control- or SCN- hematopoietic progenitor cells (HPCs)
To address how CSF3R mutations affect hematopoiesis in a severe congenital neutropenia (SCN) background we used SCN patient, or control, derived induced pluripotent stem cells (iPSC). HPCs were generated from CRISPR-Cas9 genome edited CSF3R-d715 SCN or control-derived iPSCs with the STEMdiff™ Hemato...
ORGANISM(S): Homo sapiens 
2021-04-01 | E-MTAB-10288 | biostudies-arrayexpress
TranscriptomicsRNA sequencing comparing SCN CSF3R-d715 RUNX1-D171N (RHD) treated with the HDAC inhibitor MS275, octyl-(R)-2hydroxyglutarate (2HG) or solvent control (DMSO)
Effects of TET2 on repressing inflammation have been assigned to its methylcytosine dioxygenase activity, but also to its ability to recruit HDAC-mediated repressor activity to pro-inflammatory genes. To discriminate between the two above-proposed functions of TET2, we asked how inhibition of its en...
ORGANISM(S): Homo sapiens 
2020-08-24 | E-MTAB-9374 | biostudies-arrayexpress
TranscriptomicsRNA sequencing comparing different stages of leukemic progression in a mouse model of severe congenital neutropenia (SCN)
To address how Csf3r and RUNX1 mutations in combination with CSF3 administration affect hematopoiesis in vivo, we performed serial transplantation experiments. Lineage-negative Csfr-d715 BM cell cells were lentivirally transduced with the patient specific RUNX1-D171N (RHD) mutant or an empty vector ...
ORGANISM(S): Mus musculus 
2020-08-24 | E-MTAB-9377 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of Acute Myeloid Leukemia Cell lines with a 3q-aberration and Acute Myeloid Leukemia cell line controls
Using RNA deep sequencing we determined gene expression patterns and expression genotypes in Acute Myeloid Leukemia (AML) cell lines harboring a 3q-aberration. These cell lines specifically overexpress the gene EVI1 which plays a significant part in leukomogenesis. Additionally we RNA sequenced AML ...
ORGANISM(S): Homo sapiens 
2014-04-03 | E-MTAB-2225 | biostudies-arrayexpress
TranscriptomicsRNA sequencing comparing the effect of the introduction of RUNX1-D171N (RHD) in control- or SCN -CSF3R-d715 hematopoietic progenitor cells (HPCs)
To address how CSF3R and RUNX1 mutations affect hematopoiesis in a severe congenital neutropenia (SCN) background we used SCN patient, or control, derived induced pluripotent stem cells (iPSC). HPCs were generated from CRISPR-Cas9 genome edited CSF3R-d715 SCN or control-derived iPSCs with the STEMdi...
ORGANISM(S): Homo sapiens 
2020-08-24 | E-MTAB-9375 | biostudies-arrayexpress
TranscriptomicsRNA sequencing comparing the transcriptome of a severe congenital neutropenia (SCN) patient who progressed to AML (SCN-AML) with the SCN phase and healthy controls
CD34+ hematopoietic stem progenitor cells (HSPCs) from cryo-preserved blood or bone marrow were FACS sorted in TriZol and RNA was isolated according to the manufacturer’s protocol. SMARTer Ultra Low Input RNA kit for sequencing (Clontech, v4 Cat# 634891) was used to generate cDNA. Sequencing librari...
ORGANISM(S): Homo sapiens 
2020-08-24 | E-MTAB-9381 | biostudies-arrayexpress
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