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Genes affected by PAD4 deficiency in LSK cells obtained from mouse bone marrow.

ABSTRACT: We found PAD4, which is one of the transcriptional co-regulator by histone modification, was highly expressed in lineage-, Sca-1+, c-kit+ (termed as LSK) cells of mouse bone marrow. To find the target genes which are regulated by PAD4 in LSK cells, we analyzed gene expression in PAD4-deficient mouse as compared with wild-type mouse. Gene expression in wild-type and PAD4-deficient LSK cells

ORGANISM(S): Mus musculus

SUBMITTER: Katsuhiko Nakashima

PROVIDER: E-GEOD-45482 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genes affected by PAD4 deficiency in LSK cells obtained from mouse bone marrow.

Project description:We found PAD4, which is one of the transcriptional co-regulator by histone modification, was highly expressed in lineage-, Sca-1+, c-kit+ (termed as LSK) cells of mouse bone marrow. To find the target genes which are regulated by PAD4 in LSK cells, we analyzed gene expression in PAD4-deficient mouse as compared with wild-type mouse.

2013-06-01 | GSE45482 | GEO

Gene therapy of Mpl -/- mouse LSK cells

Project description:Comparison of Mpl-/- mouse LSK cells, either treated with control (GFP) or Mpl lentivirus. Lineage negative bone marrow cells were isolated and transduced and transplanted into Mpl-/- recipient mice. After transplantation and follow up mice were sacrificed and LSK (lineage negative, Sca-1 positive, cKit positive) cells were isolated by FACS. RNA was isolated using RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany) and RNA was amplified for microarray hybridization using the Nugen Ovation system (Nugen Technologies, AC Bemmel, Netherlands). The resulting material was hybridized to Affymetrix Mouse 430 2.0 arrays. RMA normalization and summarization was performed in R 2.10 using Bioconductor packages. The aim was to show the normalization of Mpl associated gene expression. 3 control (GFP transduced) samples of Mpl -/- mouse LSK cells and 3 treatment (Mpl transduced) samples of Mpl -/- mouse LSK cells.

2011-01-03 | E-GEOD-26403 | biostudies-arrayexpress

RNA-Seq analysis of wild-type and Brpf1-null fetal liver LSK cells

Project description:To compare the impact of hematopoietic-specific Brpf1 gene inactivation, LSK (Lin-Sca1+cKit1+) cells were sorted from wild-type and Brpf1-null fetal liver cells for RNA-Seq. Four E14.5 embryos were used to pool sufficient LSK cells for total RNA isolation and subsequent sequencing on HiSq2500. Two independent pairs of wild-type and mutant RNA samples (each of which contained LSK cells pooled from four embryos) were used for oligo-dT primed RNA Seq.

2016-08-10 | E-GEOD-83483 | biostudies-arrayexpress

Identify gene expression signatures in the niche cells (CD45 negative) during proliferation of Hematopoietic stem cells (LSK)

Project description:To further identify gene expression signatures in the niche cells (CD45 negative) during proliferation of Hematopoietic stem cells (LSK), we employed mice whole genome (60K) microarray expression profiling as a discovery platform to identify the up-regulated and down-regulated genes of the niche. [Samples A-D] In this experiment a physiological stress model was created where the recipient mice were subjected to sub lethal radiation (700 CGy) following a transplantation of 30,000 LSK cells (HSCs). Bone marrow cells were isolated on day 0 (before transplantation) and day 10 (post transplantation of 30,000 LSK cells when maximum proliferation of HSCs was observed). Donor HSCs was sorted by FACS following RNA isolation and cDNA synthesis followed by single color global gene expression analysis. Agilent one-color experiment,Organism:Mouse, Agilent Whole Genome Mouse 8x60k (AMADID: 26986) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2016-07-03 | E-GEOD-75294 | biostudies-arrayexpress

Gene expression analysis of Cbp deficient LSK cells

Project description:The transcriptional coactivator Cbp is critical for hematopoietic stem cell (HSC) development. However, its role in adult HSC and the mechanistic detail of Cbp control of HSC function remains unknown. Using conditional deletion of Cbp in the adult HSC compartment, we demonstrate an altered balance between differentiation and self-renewal with gradual loss of phenotypic HSC, differentiation defects in lower compartments and the development of myeloid malignancies. In addition, we demonstrate that Cbp -/- HSCs reconstitute hematopoiesis with lower efficiency than their wild type counterparts and readily exhaust over time when placed under the replicative stress of serial transplantation. Furthermore, we demonstrate abnormal cell cycle (re)entry and apoptosis in HSC which, with preferential differentiation, also contribute to stem cell exhaustion. Finally we demonstrate global transcriptional abnormalities predicted to alter cell cycle control, balanced differentiation and HSC function upon Cbp deletion and link Cbp to a critical HSC transcriptional regulatory network through genome-wide analysis of Cbp binding. Genome-wide gene expression analysis of LSK population after Cbp deletion. The LSK population of bone marrow is enriched for hematopoietic stem cells. Total RNA was extracted from flow-sorted LSK population of bone marrow, 4 weeks after pIpC induced deletion of Cbp. 2 replicates for Cbp wt control, 2 replicates for Cbp Mx.

2011-12-15 | E-GEOD-25268 | biostudies-arrayexpress

Gene expression in WT and Ikaros-deficient LSK cells

Project description:The Ikaros zink finger transcription factor is a critical regulator of the hematopietic system, and plays an important role in the regulation of the development and function of several blood cell lineages. We used microarrays to characterize how Ikaros deficieny affects global transcription in the hematopoietic stem and progenitor cells from wild-type and Ikaros mutant mice. lin- Sca1+ c-Kit+ (LSK) cells, that contains the hematopoietic stem cells and the multipotent progenitor cells, were sorted by FACS from the bone marrow of 6-7 weeks old WT and IkL/L mutant mice. Total RNA extracted from these cells was subjected to transcriptome analysis.

2015-11-03 | E-GEOD-61147 | biostudies-arrayexpress

Transcriptional profiling of Cebpa knock-in mutant LSK hematopoietic stem cells

Project description:Gene expression of LSK (lin-Sca-Kit+) hematopoietic stem cells from wild type mice was compared with LSK from Cebpa knock-in mutant mice (K/K, K/L, and L/L mutants). Fetal liver cells for each genotype were competitively transplanted into irradiant recipients. Donor-derived LSK cells were isolated by FACS sorting of recipient bone marrow. 3 biological replicates of each were generated and expression profiles were determined by hybridization to Affymetrix Moe430_2 arrays.

2009-11-03 | E-TABM-695 | biostudies-arrayexpress

Transcriptional profiling of mouse LSK cells from conditional null Fog1 mutants

Project description:Gene expression of LSK cells from wild type mice was compared with those from conditional null mutants (Fog1 Floxed). Cre excision in mutant mice was induced with polyIC. LSK cells were isolated by FACS. Expression profiles of biological replicates were determined by hybridization to Affymetrix MoGene 1.0 ST arrays.

2011-08-03 | E-MTAB-343 | biostudies-arrayexpress

Expression data from WT and GABPalpha-deficient Flt3(-) LSK cells

Project description:GABPalpha is an Ets family transcription factor and involved in regulation of both basic cellular functions such as cell cycle progression and tissue-specific biological processes. We found that GABPalpha is critically required for survival and differentiation of hematopoietic stem cells. We used microarrays to detect gene expression changes in Flt3(-) LSK cells (which contains both long-term and short-term hematopoietic stem cells) by GABPalpha deficiency. Mx1Cre-GABPa(FL/+) and Mx1Cre-GABPa(FL/-) mice were treated with pIpC to induce inactivation of GABPalpha in bone marrow cells. Four days after last treatment of pIpC, the bone marrow cells were isolated and the Flt3(-)LSK subset was purified by cell sorting. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

2011-07-27 | E-GEOD-23341 | biostudies-arrayexpress

Gene expression profiling of control cohesin knockdown LSK cells

Project description:We performed RNA-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for Renilla, Smc1a or Stag2. RNA-sequencing control (Renilla) and cohesin (Smc1a and Stag2) knockdown cells.

2015-09-16 | E-GEOD-72369 | biostudies-arrayexpress

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