Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Determination of HOXA1 and HOXA9 target genes with inducible HOX constructs

ABSTRACT: Target genes of HOXA1 and HOXA9 were determined with the help of inducible HOX-ER constructs. For this purpose bone marrow was harvested from C57BL/6 mice and c-Kit positive progenitors were enriched by magnetic sorting (MACS technology, Miltenyi, Germany). After retroviral infection by spinoculation the cells were plated for three rounds in methylcellulose. Subsequently cells were maintained in liquid culture in RPMI1640 supplemented with murine recombinant cytokines at 100ng/ml (stem cell factor) and 10ng/ml (IL-3, IL-6, granulocyte/macrophage-colony stimulating factor) as well as 100nM 4-hydroxy-tamoxifen (TAM) for HOX activation.

For microarray analysis 4 independent cell lines were created for each HOX construct. RNA was isolated from cells in the presence of TAM and 72h after withdrawal of the inductor. Pairs of RNA replicates were pooled and two +TAM as well as two -TAM duplicates per HOX gene were hybridized to Agilent44K mouse expression arrays. Array processing and evaluation was done commercially according to Agilent specifications by ImaGenes (now SourceBioScience), Berlin, Germany.

ORGANISM(S): Mus musculus

SUBMITTER: Robert Slany

PROVIDER: E-MEXP-3648 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

HOX genes regulate Rac1 activity in hematopoietic cells through control of Vav2 expression.

Breitinger C C Maethner E E Garcia-Cuellar M-P MP Schambony A A Fischer K D KD Schilling K K Slany R K RK

Leukemia 20120620 1

PMID: 22713647

Similar Datasets

Homeodomain dependent gene expression in HOX transformed primary cells

Project description:The gene expression profile was determined in primary cells transformed by two different HOX genes (HOXA1 and HOXA9) and by two HOX derivatives where the homeodomain was exchanged.

2013-01-31 | E-MEXP-3617 | biostudies-arrayexpress

Roles of Cofactors and Chromatin Accessibility in Hox Protein Target Specificity

Project description:Regulation of specific target genes by transcription factors is central to gene network control in development. How target specificity is achieved in eukaryotic genomes is poorly understood, as exemplified by the Hox family, which show limited in vitro DNA-binding specificity but clear functional specificity in vivo. We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. Ubx and Abd-A bind to similar target sites in accessible chromatin whereas Abd-B binds additional specific targets. Provision of the TALE class cofactors, Exd and Hth, alters the Ubx binding profile, enabling binding to additional targets in the genome. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in relatively DNase1 inaccessible chromatin, suggesting that competition with nucleosomes is a key factor determining Hox protein target specificity. This ChIP-Seq study performed on Kc167 cells involves two experiments and 6 ChIP samples. In Experiment 1, we generated genome-wide binding profiles for Ubx, Abd-A and Abd-B. An equal volume of input chromatin was retained from each of the Hox samples and combined to represent the input, which was purified alongside the ChIP samples. We performed two biological replicates for each sample. Sequencing was performed using the Illumina MiSeq platform. In Experiment 2, we generated genome-wide binding profiles for Ubx, mutant Ubx and Ubx in the presence of Hth. We performed two biological replicates for each sample except Ubx where we performed just one. Sequencing was performed using the Illumina HiSeq 2000 platform. For all samples, Experiment 1 input chromatin was used as the reference control to assay ChIP enrichment.

2015-12-07 | E-GEOD-69796 | biostudies-arrayexpress

Discovery of Tamoxifen and N-Desmethyl Tamoxifen Protein Targets in MCF-7 Cells Using Large-Scale Protein Folding and Stability Measurements

Project description:The proteins in an MCF-7 cell line were probed for tamoxifen (TAM) and n-desmethyl tamoxifen (NDT) induced stability changes using the Stability of Proteins from Rates of Oxidation (SPROX) technique in combination with two different quantitative proteomics strategies. Together the SILAC- and iTRAQ-SPROX experiments described here enabled over 1000 proteins to be assayed for TAM- and NDT- induced protein stability changes, and a total of 163 and 200 protein hits were identified in the TAM and NDT studies, respectively. A subset of high confidence hits were assessed for experimental links to the ER using a STRING analysis. TAM was shown to induce stabilization of Y-box binding protein 1 (YBX1), a protein recently shown to bind the estrogen receptor. TAM was shown to directly interact with purified recombinant YBX1 with Pulse Proteolysis (PP). These results support YBX1 as a direct protein target of TAM. Proteins with altered expression levels with TAM and NDT treatment were identified with SILAC quantitation. In total, 799 and 671 proteins were probed for TAM- and NDT- induced expression changes, respectively, and 49 and 30 proteins had altered expression. This work also involved the use of a novel data analysis strategy to identify protein targets of ligands using the SPROX technique.

2019-11-08 | PXD006732 | Pride

Affymetrix SNP array data for xenografted transient abnormal myelopoiesis samples

Project description:Transient abnormal myelopoiesis (TAM) is a clonal pre-leukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, IL-2Rγnull mice. In serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from murine bone marrow (hCD45 sorted) or human peripheral blood samples. Copy number analysis of Affymetrix 500K SNP arrays was performed for xenografted TAM samples of 3 patients. There are also 3 samples from TAM patients in remission, which were used as references for copy number inference.

2013-03-01 | E-GEOD-44739 | biostudies-arrayexpress

Endocytic and signalling function of stabilin-1 in tumor associated macrophages

Project description:Stabilin-1 is a scavenger/sorting receptor expressed by sinusoidal endothelial cells, alternatively-activated and tumor-associated macrophages (TAM) in several types of human cancer and mouse tumor models. We have found abundant expression of stabilin-1 on TAM in mouse model of mammary adenocarcinoma (TS/A) We performed microarrays with TAM isolated from wild type (wt) and stabilin-1 knock out (ko) mice in order to examine if stabilin-1 affects gene expression in TAM using mouse model of TS/A mammary adenocarcinoma Balb/c Wt and stabilin-1 ko female mice (8-12 weeks old) were inoculated s.c. with 5x10e6 TS/A cells. TAM were isolated from TS/A tumors 21 days after tumor challenge using CD11b MACS beads (Miltenyi Biotec), lysed for RNA and used for microarrays. Samples from 3 wt and 3 stabilin-1 ko mice were analyzed.

2014-10-30 | E-GEOD-55595 | biostudies-arrayexpress

Discovery of Tamoxifen and N-Desmethyl Tamoxifen Protein Targets in MCF-7 Cells Using Large-Scale Protein Folding and Stability Measurements, part 2

2019-11-08 | PXD006747 | Pride

ChIP-seq of CD117-positive primary hematopoietic precursor cell from Meer mice that carry a leukemogenic knock-in of an inducible ENL-ER portion into the mouse Mll locus

Project description:This ChIP-seq experiment was done to investigate the global distribution of H2A ubiquitination (a hallmark of polycomb mediated repression), H2B ubiquitination (introduced by PAF-complex associated ubiquitin ligases and connected to active transcription), and PAF1 occupation in Meer cells. Meer cells are primary cells transformed by a knock-in of an inducible Mll-ENL oncogene. ENL and ENLins ChIP-seqs were done in CD117-positive primary hematopoietic cells without any pretransformation by other oncogenes.

2018-01-23 | E-MTAB-5569 | biostudies-arrayexpress

Characterization of the molecular signature associated with the ablation of integrin Î±6 in IECs in the Î±6ÎIEC-TAM mouse model

Project description:Transcriptome analysis of mRNAs extracted from the rectal mucosa of WT and Î±6ÎIEC-TAM mice, 15 days after tamoxifen treatment Inflammatory bowel diseases (IBD) in humans are characterized by chronic inflammation and gastrointestinal tissue damage, caused by a combination of genetic and environmental factors. We show that the specific ablation of integrin Î±6 in intestinal epithelial cells (IECs) results in spontaneous colorectal inflammation in mice. In order to characterize the earlier molecular signature involved in the onset of inflammation, we performed Affymetrix microarrays and compare control versus Î±6ÎIEC-TAM transcriptomes after tamoxifen treatment. RNAs were prepared from rectal mucosa of 3 control mice treated with tamoxifen, 4 mutant mice treated with tamoxifen and 4 mutant mice treated with NaCl. The transcriptome analysis was performed using the Affymetrix Mouse Gene 1.0 ST arrays. Images were processed using affymetrix GeneChipÂ® Command ConsoleÂ® Software (AGCC) (version 2.0) and numerical values were generated using Affymetrix Expression Consoleâ¢ Software (version 1.1).

2016-07-07 | E-GEOD-70700 | biostudies-arrayexpress

Under conditions of hormonal adjuvant treatment the estrogen receptor apoprotein supports breast cancer cell cycling through the retinoic acid receptor M-NM-11 apoprotein

Project description:Under conditions of hormonal adjuvant treatment the estrogen receptor apoprotein supports breast cancer cell cycling through the retinoic acid receptor M-NM-11 apoprotein. Basal proliferation persisted in estrogen-sensitive breast cancer cells grown in hormone depleted conditioned media without or with 4-hydroxytamoxifen (OH-Tam). Downregulating ER using siRNA inhibited basal proliferation by promoting cell cycle arrest. The basal expression of RARM-NM-11, the only RARM-NM-1 isoform that was expressed in breast cancer cell lines and in most breast tumors, was supported by apo-ER but was unaffected by OH-Tam. The overlapping tamoxifen-insensitive gene regulation by apo-ER and apo-RARM-NM-11 comprised activation of mainly genes promoting cell cycle and mitosis and suppression of genes involved in growth inhibition. Cells were plated at 20% confluence in low glucose phenol red free medium supplemented with 5% charcoal stripped FBS and glutamine 24h-48h prior to transfection. Treatment with vehicle, OH-Tam (100nM), or OH-Tam (500nM) was begun an additional 24h later. Cells were transfected with control siRNA, ERM-NM-1 siRNA or RARM-NM-1 siRNA.

2011-05-13 | E-GEOD-26298 | biostudies-arrayexpress

Multiplexed DNA high throughput genotyping study to determine the mutational status of transient (TAM) and acute myeloid leukaemic (ML-DS) Down syndrome individuals.

Project description:We used a 48.48 Fluidigm Access Array approach (1070 Amplicons spanning 62 genes: 157kB coverage) of genomic DNA from over 100 samples to genotype individuals with transient abnormal myelopoiesis (TAM) and acute myeloid leukemia of Down syndrome (ML-DS). Individually barcoded patient samples were subjected to paired-end 150bp sequencing (Illumina MiSeq), including paired GATA1 variant negative controls (including Post treatment) and 8 known reference GATA1- controls. Samples were mapped to build 37 of the human reference genome and subject to bioinformatic analysis (Varscan, Pindel, GATK) to facilitate the characterisation of known gene mutations in cancer as well as the identification / validation of potentially novel variants.

2019-07-17 | E-MTAB-7729 | biostudies-arrayexpress

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