Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from Hematopoietic stem cells

ABSTRACT: Objective: Microarray analysis was used to determine the molecular mechanism underlying Fancd2 and Foxo3a double knockout mice HSCs exhaustion. Methods: SLAM cells were obtained from WT, Fancd2KO, Foxo3aKO and DKO bone marrow cells. Total RNA from SLAM cells was purified by RNeasy kit (Qiagen) following the manufacturer’s procedure. And then the RNA was fluorescently labeled and hybridized to Affmetrix Mogene 2.0 ST array. Data was analyzed by Genespring GX11 software. Results: a large proportion of differentially expressed genes in dKO HSCs belonged to cell cycle control. Another group of up-regulated genes were those involved in the differentiation of HSCs. Other differentially regulated transcripts included genes known to be involved in oxidative stress response, or to have roles in DNA repair. Conclusion: Cell cycle, DNA repair, DNA binding and hematopoietic lineage differentiation pathways might have been perturbed in HSC exhaustion. Mouse Femurs and tibias from WT, Fancd2KO, Foxo3aKO and DKO mice were flushed to dissociate the BM fraction. The mononuclear cells were isolated by Ficoll (GE Healthcare) gradient centrifugation. Single SLAM (Lin-ckit+Sca-1+CD34-) cells were sorted. RNA was extracted, labelled, and quantified using the Mouse ST-2 microarray.

ORGANISM(S): Mus musculus

SUBMITTER: Xiaoli Li

PROVIDER: E-GEOD-64215 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from Hematopoietic stem cells

Project description:Objective: Microarray analysis was used to determine the molecular mechanism underlying Fancd2 and Foxo3a double knockout mice HSCs exhaustion. Methods: SLAM cells were obtained from WT, Fancd2KO, Foxo3aKO and DKO bone marrow cells. Total RNA from SLAM cells was purified by RNeasy kit (Qiagen) following the manufacturer’s procedure. And then the RNA was fluorescently labeled and hybridized to Affmetrix Mogene 2.0 ST array. Data was analyzed by Genespring GX11 software. Results: a large proportion of differentially expressed genes in dKO HSCs belonged to cell cycle control. Another group of up-regulated genes were those involved in the differentiation of HSCs. Other differentially regulated transcripts included genes known to be involved in oxidative stress response, or to have roles in DNA repair. Conclusion: Cell cycle, DNA repair, DNA binding and hematopoietic lineage differentiation pathways might have been perturbed in HSC exhaustion.

2014-12-17 | GSE64215 | GEO

Expression data from mouse E14.5 fetal liver SLAM LSKs

Project description:To determine genes in FL HSCs that are sensitive to Notch signagling, E14.5 FL cells were cultured on DL1( to stimulate Notch signaling). Cells were cultured in the presence of DMSO (vehicle control) or gamma secretase inhibitor (1uM) for 4 hrs or 10hrs. Gamma secretase inhibitor was used to inhibit Notch signaling. SLAM-LSKs were sorted and used for RNA preparation. 7 biological replicates (14 totalt samples) were collected for cells cultured for 4hrs. 4 biological replicates (8 total samples) were collected from cells cultured for 10hrs. Each replicate consisted of a DMSO and GSI treated sample

2014-01-28 | E-GEOD-53713 | biostudies-arrayexpress

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - SLAM - seq

Project description:Pulse-chase experiment using SLAM-seq in WT, PHF3KO, and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7898 | biostudies-arrayexpress

HSC expression array

Project description:Increased expression of Kruppel like factor 7 (KLF7) is an independent predictor of poor outcome in pediatric acute lymphoblastic leukemia. The contribution of KLF7 to hematopoiesis has not been previously described. Herein, we characterized the effect on murine hematopoiesis of the loss of KLF7 and enforced expression of KLF7. Long-term multilineage engraftment of Klf7-/- cells was comparable to control cells, and self-renewal, as assessed by serial transplantation, was not affected. Enforced expression of KLF7 results in a marked suppression of myeloid progenitor cell growth and a loss of short- and long-term repopulating activity. Interestingly, enforced expression of KLF7, while resulting in multi-lineage growth suppression that extended to hematopoietic stem cells and common lymphoid progenitors, spared T cells and enhanced the survival of early thymocytes. RNA expression profiling of KLF7-overexpressing hematopoietic progenitors identified several potential target genes mediating these effects. Notably, the known KLF7 target Cdkn1a (p21Cip1/Waf1) was not induced by KLF7, and loss of CDKN1A does not rescue the repopulating defect. These results suggest that KLF7 is not required for normal hematopoietic stem and progenitor (HSPC) function, but increased expression, as seen in a subset of lymphoid leukemia, inhibits myeloid cell proliferation and promotes early thymocyte survival. HSC expression array: Lin- c-Kit+ Sca-1+ CD150+ CD48- CD41- cells were sorted from wild-type C57Bl/6 mice and RNA expression analyzed. RNA expression in KLS SLAM cells. KLS-SLAM cells were sorted from 6-10 week old C57Bl/6 mice

2012-08-24 | E-GEOD-40324 | biostudies-arrayexpress

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - Targeted SLAM-seq

Project description:Tergeted SLAM seq of WT, PHF3 KO and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7899 | biostudies-arrayexpress

JAK2V617F mutant HSC microarray

Project description:Mutant JAK2V617F is found in majority of patients with myeloproliferative neoplasm. While heterozygous JAK2V617F induced an ET-like phenotype, JAK2V617F homozygosity drives an severe PV-like phenotype in knock-in mice. HSCs from mice with homozygous JAK2V617F expression show impaired self-renewal in transplants. To understand the molecular mechanisms involved this HSC functional defect, microarray was performed on isolated LT-HSCs from mice expressing wildtype, heterozygous and homozygous expression of mutant JAK2.

2018-08-06 | E-MTAB-6878 | biostudies-arrayexpress

Role of de novo DNA methyltransferases in hematopoietic stem cells (WGBS)

Project description:To investigate the global DNA methylation changes in Dnmt3a-KO and Dnmt3ab-dKO HSCs compared to control HSCs, we performed whole genome bisulfite sequencing Mouse hematopoietic stem cell DNA methylation profiles of control, Dnmt3a-KO and Dnmt3ab-dKO HSCs were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

2014-08-19 | E-GEOD-50780 | biostudies-arrayexpress

The DNA Double-Strand Break Response Is Abnormal in Myeloblasts From Patients With Therapy-Related Acute Myeloid Leukemia

Project description:In order to examine if the upregulation of DNA repair genes on chromosome 8 was associated with the abnormal DSB phenotype observed in trisomy 8 (defined by array CGH or cytogenetics), we compared the mRNA levels of DNA repair genes on chromosome 8 in trisomy 8 t-AML patients versus normal t-AML gammaH2AX responders using gene expression array data. Bone marrow cells taken directly from patients after written informed consent were cryopreserved, RNA extracted, and microarray analysis was performed using Affymetrix U133plus2 chips.

2013-11-19 | E-GEOD-52478 | biostudies-arrayexpress

Role of de novo DNA methyltransferases in hematopoietic stem cells (RNA-seq)

Project description:To investigate the global transcriptome expression in Dnmt3ab dKO HSCs, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total for each genotype of HSC were obtained. Mouse hematopoietic stem cell mRNA profiles of Dnmt3ab Dko HSCs, generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

2014-08-19 | E-GEOD-50775 | biostudies-arrayexpress

Genome wide analysis of acral melanoma (Affymetrix)

Project description:Genotyping of a matched normal, primary and metastatic acral melanoma DNA from blood and one matched Primary and one metastatic acral melanoma was genotyped on Affmetrix SNP6

2011-12-13 | E-GEOD-28910 | 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