Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of umbilical cord blood cells upon knockdown of NAP1L3

ABSTRACT: The nucleosome assembly proteins (NAPs) are histone chaperones with an important role epigenetic regulation of gene expression. We find that high gene expression levels of murine Nap1l3 is restricted to hematopoietic stem cells. Loss of function of murine and human NAP1L3 impair maintenance of hematopoietic stem cells and differentiation both in vitro and in vivo. NAP1L3 inhibition in human hematopoietic cells causes a growth arrest in the G0 phase of cycle progression, and induces gene expression signatures that highly significantly correlate with downregulation of genes involved in cell cycle regulation, including E2F and MYC target genes. In addition, we also show that the HOXA3, HOXA5, HOXA6 and HOXA9 are markedly upregulated when NAP1L3 is suppressed in Human hematopoietic cells. Taken together, our findings establish an important role for NAP1L3 in HSC homeostasis and hematopoietic differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE106170 | GEO | 2017/10/26

SECONDARY ACCESSION(S): PRJNA415805

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome profiling of hematopoietic cells derived from human pluripotent stem cells

Project description:We performed morphogen-directed differentiation of human PSCs into HE followed by combinatorial screening of 26 candidate HSC-specifying TFs for the potential to promote hematopoietic engraftment in irradiated immune deficient murine hosts. We recovered seven TFs (ERG, HOXA5, HOXA9, HOXA10, LCOR, RUNX1, SPI1) that together were sufficient to convert HE into hematopoietic stem and progenitor cells (HSPCs) that engraft primary and secondary murine recipients.

2017-05-17 | GSE83719 | GEO

inDrop single cell RNA-seq of hematopoietic cells derived from human pluripotent stem cells

2017-05-17 | GSE85111 | GEO

Gene expression of human colon cancer HCT116 cells [HOXA5_OE]

Project description:Abberant expression of HOXA5 is implicated in cancer development. We identified a novel long non-coding RNA (HOXA5 short RNA) transcribed from HOXA6-HOX5 locus using a next generation-based target RNA capture system. In this study, HCT116 cells were overexpressed with a vector containing HOXA5 short RNA. Gene expression levels of these cells were measured by microarray analysis.

2019-06-20 | GSE124478 | GEO

Gene expression of human colon cancer HCT116 cells [HOXA5_si]

Project description:Abberant expression of HOXA5 is implicated in cancer development. We identified a novel long non-coding RNA (HOXA5 short RNA) transcribed from HOXA6-HOX5 locus using a next generation-based target RNA capture system. In this study, HCT116 cells were treated with siRNAs targeting the novel non-coding RNA. Gene expression levels of these cells were measured by microarray analysis.

2019-06-20 | GSE124479 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) HSCs and NHD13+ MDS HSCs Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. To determine the molecular mechanism of severe cytopenia in NHD13+ Tg mice, we purified Lin-Sca-1+c-Kit+CD34-Flt3-CD150+ HSCs from WT and NHD13+Tg mice at 4 month of age and perform the RNA-seq analysis. Methods: Trizol was used to extract RNA from FACS sorted CD150+CD34–Flt3–LSK viable cells. Total RNA was used for quality controls and for normalization of starting material. cDNA-libraries were generated with 10 ng of total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing according to the manufacturer’s indications. Sequencing was done using the Illumina Next-Gen Sequencing HiSeq platform with 30-45 million 75bp, paired-end reads. Results: We found 597 genes with significantly differential expression in NHD13+ HSCs, compared to WT controls (p<0.001). The expression of NUP98-HOXD13 up-regulated the expression of HOX genes, including Hoxa3, Hoxa5, Hoxa7, Hoxa9, Hoxb6, Hoxc5, Hoxc6, Hoxc8, Hoxc9 and Hoxd3, the important myeloid transcription factor Pbx3, cell cycle regulators, Cdk6 and Cdc25C, as well as the transcripts encoding the Ly6d surface membrane protein. We then performed pathway analyses, which showed that DNA duplication, DNA damage response and cell cycle-related genes, were more highly expressed in NHD13+ HSCs than WT HSCs, while multiple metabolic process-related gene pathways were downregulated. Conclusions: Our analyses demonstrate that the gene expression signature defined in murine NHD13+ MDS HSCs displays robust similarities with the gene expression profiles of human MDS cells, strongly suggesting that this murine MDS model can be used to accurately model human MDS.

2018-04-17 | GSE97911 | GEO

Expression data from murine cell line transduced with epitope tagged forms of Hoxa9

Project description:Importantly increasing evidence shows that Hox genes such as Hoxa9 are key regulators of stem cell self-renewal and hematopoiesis. Hoxa9 is expressed in early hematopoietic progenitor cells and promotes stem cell expansion. In contrast Hoxa9 down regulation is associated with hematopoietic differentiation. In addition to its role in development, HOXA9 has been intensively studied because of its central role in human acute leukemias. Despite their obvious biomedical importance, the mechanisms through which Hoxa9 and its partner proteins exert their downstream functions are poorly understood. Using whole-genome gene expression profiling, we identified direct targets of Hoxa9 in murine MHPs after 4-OHT withdraw, resulting in cell differentiation.

2011-02-01 | GSE21299 | GEO

Genes regulated by HoxA3 in endothelial and hematopoietic progenitors

Project description:We used a murine ES cell line in which HoxA3 expression is under control of a tetracycline-responsive element and differentiated these cells as embryoid bodies (EBs). Endothelial (Flk-1 VE-cadherin double positive, FV) and hematopoieitc progenitors (c-Kit CD41 double positive, K41) were isolated from differentiated EBs that had been induced for 6 hours by doxycycline (Dox) treatment. Here we show genes regulated upon HoxA3 upregulation (6 hours doxycycline treatment) in hematopoietic and endothelial progenitors.

2010-12-20 | E-GEOD-25080 | biostudies-arrayexpress

Epistasis analysis of Runx1 and Gata1 over HoxA3 in hemogenic endothelium

Project description:We observe that HoxA3 represses hematopoieis by the repression of several transcription factors including Runx1 and Gata1. Up regulation of either Runx1 or Gata1 in the presence of HoxA3 reverted the hematopoietic repression. We have performed full genome analysis to determine the molecular signature of hematopoietic development in response to upregulation of Runx1 and Gata1. Endothelial progenitors were sorted from HoxA3 induced EBs, transduced with either control vector (control), Runx1 vector or Gata1 vector. Cells were co-cultured on Op9 for 5 days: in the following conditions: Control, HoxA3 upregulation, HoxA3 + Runx1 upregulation, HoxA3 + Gata1 upregulation in triplicate. After 5 days of culture,transduced cells were sorted (5000 cells) and prepared for microarray.

2010-12-20 | E-GEOD-25079 | biostudies-arrayexpress

Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes

Project description:EpiSELEX-seq method was used to characterize the binding preference of human TF complexes to methylated DNA, including BZIP proteins ATF4 and CEBPb, homeodomain TF heterodimers of HM(Meis1)-Pbx1 together with either HoxA1, HoxA5 or HoxA9 and tumor suppressor protein p53.

2017-06-13 | GSE98652 | GEO

Effect of glomerular disease on the podocyte cell cycle

Project description:Proteomic data from three populations of sorted murine podocytes using the FUCCI (fluorescence ubiquitination cell cycle indicator) Cell Cycle Sensor: Wild-Type podocytes at G0 (WT_G0), Alport Syndrome podocytes at G0 (AS_G0), and Alport Syndrome podocytes at G1 (AS_G1). Cell populations were sorted from murine kidney; ~10K cells were prepared using the MicroPOTS protocol (PMID: 30460388), digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MaxQuant.

2021-01-15 | MSV000086705 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data