Microarray analysis of human hematopoietic stem cells (HSC) treated or not with antioxidants and cultured 2 days against uncultured HSC
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Applied Biosystems
ORGANISM(S): Homo sapiens
SUBMITTER: Marie-Laure Arcangeli
PROVIDER: E-MTAB-12121 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:HSC-3-5 cells, which drived from human HSC-3 cells via transwell invasion assay was high invasive.Tumor cells were injected into the tongue of SCID mice. After 1 week, transcriptional profiling of human HSC-3 tumor comparing with high invasive HSC-3-5 tumor. Goal was to determine the effects of invasion on global HSC-3-5 gene expression during tumor metastasis. HSC-3 and HSC-3-5 oral cancer cells were respectively injected into the tongue of SCID mice. After 1 weeks, total RNA was respectively extracted from the tumor tissue on tongue of SCID mice for gene expression profiling during metastasis. Briefly, two-condition experiment,HSC-3 vs. HSC-3-5 cells.
2013-08-13 | E-GEOD-39725 | biostudies-arrayexpress
Project description:HSC-3-5 cells were derived from human HSC-3 cells via transwell invasion assay. Transcriptional profiling of human HSC-3 cells comparing with high invasive HSC-3-5 cells. Goal was to determine the effects of invasion on global HSC-3-5 gene expression during tumor metastasis. Two-condition experiment, HSC-3 vs. HSC-3-5 cells.
2013-08-13 | E-GEOD-39723 | biostudies-arrayexpress
Project description:HSC-3-5 cells, which drived from human HSC-3 cells via transwell invasion assay was high invasive.Tumor cells were injected into the flank of SCID mice. After 6 weeks, transcriptional profiling of human HSC-3 tumor comparing with high invasive HSC-3-5 tumor. Goal was to determine the effects of invasion on global HSC-3-5 gene expression during tumor metastasis. HSC-3 and HSC-3-5 oral cancer cells were respectively injected into the flank and tongue of SCID mice. After 1 and 6 weeks, total RNA was respectively extracted from the tumor tissue on tongue and flank of SCID mice for gene expression profiling during metastasis. Briefly, two-condition experiment,HSC-3 vs. HSC-3-5 cells.
2013-08-13 | E-GEOD-39726 | biostudies-arrayexpress
Project description:All living cells rely on the communication with other cells to ensure their function and survival. Molecular signals are sent among cells of the same cell type and from cells of one cell type to another. In cancer, not only the cancer cells themselves are responsible for the malignancy, but also stromal (non-cancerous) cells and the molecular signals they send to cancer cells are important factors that determine the severity and outcome of the disease. Therefore, the identification of stromal signals and their influence on cancer cells is important when looking for novel treatment strategies. We have generated gene expression profiles of both stromal (HSC), and liver cancer (HCC) cells treated with HSC conditioned medium to elucidate cell communication from HSC to HCC cells. 15 HSC samples, 15 HCC samples treated with conditioned medium of the HSC samples, 4 control hep samples without treatment
2015-04-24 | E-GEOD-62455 | biostudies-arrayexpress
Project description:Here we tracked transcriptional changes in LT, ST-HSC and MLP after transplantation into immunocompromised mice. We show that LT- and ST-HSC activate similar pathways upon transplantation but they modulate distinct sets of genes. Total RNA was obtained from flow-sorted populations of human LT-, ST-HSC and MLP isolated from cord blood or immunocompromised mice transplanted with human at hematopoeitic progenitors at different time points after transplantation.
2015-02-20 | E-GEOD-58299 | biostudies-arrayexpress
Project description:We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor. Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression. Mouse ES with inducible Lhx2 were differentiated on OP9 stromal cells into hematopoietic lineage. On day 5 of the differentiation induction,Lhx2 expression was started by the addition of doxycycline (dox) and the cells were cultured on OP9 stromal cells in the presence of IL-6 and SCF. On day 20, HSC-like cells were harvested and re-seeded onto OP9 stromal cells in the absence of Lhx2 expression by dox-removal for 3 days. these cells were compared with the original HSC-like cells.
2013-08-26 | E-GEOD-44778 | biostudies-arrayexpress
Project description:Livers for tissue preparation and HSC isolation were derived from 2 and 22 months old male Wistar rats from Janvier Labs (France). Samples from three different lobes (median lobe, left lateral lobe, right lateral lobe) of each liver were collected and pooled for tissue analysis by gene expression. To isolate HSC, the livers were digested with enzyme solutions and HSC were enriched by density gradient centrifugation. HSC were purified by fluorescence-activated cell sorting using their typical retinoid fluorescence emitted after UV-light excitation. The sorted HSC were collected in IMDM supplemented with 10% FCS and 1 % antibiotic-antimycotic solution and cultured for 24 hours. Total RNA of HSC and whole liver tissue from 3 young and 3 old rats was extracted using the Qiagen RNeasy Mini Kit. RNA samples obtained from cultured HSC and whole liver tissues were sent to IMGM Laboratories (Martinsried, Germany) for gene expression analyses by microarrays (Affymetrix, GeneChip Rat Gene 2.0 ST Array, Thermo Fisher Scientific) in triplicates for each age group. The array data were processed by the Transcriptome Analysis Console 3.0 (Thermo Fisher Scientific).
2020-03-12 | E-MTAB-7423 | biostudies-arrayexpress
Project description:Tight regulation of hematopoietic stem cell (HSC) homeostasis is essential for life-long hematopoiesis, for preventing blood cancers and for averting bone marrow failure. The underlying mechanisms are incompletely understood. Here, we identify production of inositol-tetrakisphosphate (IP4) by inositoltrisphosphate 3-kinase B (ItpkB) as essential for HSC quiescence and function. Young ItpkB-/- mice accumulated phenotypic HSC and showed extramedullary hematopoiesis. ItpkB-/- HSC were less quiescent and proliferated more than wildtype controls. They downregulated quiescence and stemness associated mRNAs, but upregulated activation, oxidative metabolism, protein synthesis and lineage associated transcripts. Although they showed no significant homing defects, ItpkB-/- HSC had a severely reduced competitive long-term repopulating potential. Aging ItpkB-/- mice lost hematopoietic stem and progenitor cells and died with severe anemia. Wildtype HSC normally repopulated ItpkB-/- hosts, incidating a HSC-intrinsic ItpkB requirement. ItpkB-/- HSC had reduced cobblestone-area forming cell activity in vitro and showed increased stem-cell-factor activation of the phosphoinositide 3-kinase (PI3K) effector Akt, reversed by exogenous provision of the known PI3K/Akt antagonist IP4. They also showed transcriptome changes consistent with hyperactive Akt/mTOR signaling. Thus, we propose that ItpkB ensures HSC quiescence by limiting cytokine-induced PI3K signaling in HSC. For each of 3 replicate ItpkB-/- or wt samples, we enriched Lin- cells from BM of 4 pooled age-matched mice with Rapidspheres (Stemcell Technologies), FACS-sorted ?10,000 LSK CD34-CD150+CD48-Flk2- LT-HSC into lysis buffer and prepared RNA with RNeasy Micro kits (Quiagen). RNA sequencing was done using an Illumina HISeq Analyzer 2000, Casava v1.8.2 genome analyzer pipeline, TopHat v1.4.1/Bowtie2 genome alignment and Partek v6.6 mRNA annotation software. Statistical analyses were done with edgeR (Bioconductor package), excluding genes with false discovery rates >0.15, fold-change magnitudes ?1.4 and log2(counts per million) ?4 to avoid undefined values and the poorly defined log fold-changes for low counts close to 0. Unsupervised clustering of 441 significantly changed genes was done with dChip using rank correlation and a centroid linkage method. Scatter plots were generated in Spotfire. GSEA was performed with gene set permutation, using gene sets from MSigDB (www.broadinstitute.org/gsea/msigdb/index.jsp) or manually curated from, excluding genes without HUGO approved symbols
2015-03-31 | E-GEOD-56613 | biostudies-arrayexpress
Project description:Here, we present a 3’-Seq dataset of ex vivo isolated mouse multipotent hematopoietic stem cells (HSC) and multipotent progenitor cells (MPP1-4)
2020-06-01 | E-MTAB-7391 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in WASH knockout LT-HSCs, compared to the WASH WT strain. To find the reason that causes LT-HSC abnormal. Gene expression profiling using sorted LT-HSC samples from C57/BL6 strain. Total RNA extracted from WASH control (isolated RNA from WT, IRWT) and knockout mice (IRKO) were quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Each chip measures the expression level of 44, 170 genes from Mus Musculus.
2014-05-17 | E-GEOD-57741 | biostudies-arrayexpress