Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene array analysis of human CD34+ hematopoietic cells exposed during 24h to HOXB4 or HOXC4 homeoproteins

ABSTRACT: At the molecular level, the mechanisms of action of Hox genes during hematopoiesis remain elusive. Although reports have described the implication of Hox genes in some molecular pathways in mice, the targets of HOX proteins in human hematopoietic cells are mostly unidentified. Since HOXB4 and HOXC4 are transcription factors encoded by paralogous genes that display similar effects on HSCs and progenitors, we presumed that HOXB4 and HOXC4 regulate the same target genes during human HSC expansion. This hypothesis was supported by the fact that HOXB4 and HOXC4 have similar molecular structure and similar roles and expression patterns during development. To identify early factors and signaling pathways involved in hematopoietic cell expansion consecutive to the action of HOXB4 or HOXC4, we performed a differential transcriptome analysis of RNAs from cord blood-derived CD34+ cells cultured for 24 hours in the presence of MS-5 cells engineered to secrete HOXB4 or HOXC4 proteins. MS-5/GFP cells were used as control in separate co-cultures to exclude nonspecific changes in gene expression that may be associated with the presence of lentivirus-transduced MS-5 cells. Human CD34+ cord blood (4.106) cells were co-cultured for 24 hours with irradiated EGFP-, HOXB4-, or HOXC4-transduced MS-5 cells. 12 arrays were analysed. Three competitive hybridizations to the arrays were performed in duplicate using each time two dye-swap following this experimental design: AVZ056 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+GFP) AVZ059 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXB4) AVZ064 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXB4) AVZ067 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+GFP) AVZ057 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXC4) AVZ058 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+GFP) AVZ060 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+GFP) AVZ068 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXC4) AVZ061 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+HOXC4) AVZ062 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+HOXB4) AVZ065 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+HOXB4) AVZ066 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+HOXC4)

ORGANISM(S): Homo sapiens

SUBMITTER: Cathy Philippe

PROVIDER: E-GEOD-24379 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Sample groupings for this project are as follows: Cauline leaf vs Cultured Cell : - Cauline leaf, p1; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p2; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p3; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cotyledon dark : - Cotyledon, CP1; Exp:Red; Ref: Green (Cy5:Cy3) - Cotyledon, CP2; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cultured cell : - Cotyledon, cn1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon, cn2; Exp:Green; Ref: Red (Cy3:Cy5) Cotyledon dark vs Cultured cell : - Cotyledon dark, n1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n2; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n3; Exp:Green; Ref: Red (Cy3:Cy5) Germinating seed vs Cultured cell : - Germinating seed, gn1; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn2; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl light vs Hypocotyl dark : - Hypocotyl, hldn1; Exp:Red; Ref: Green (Cy5:Cy3) - Hypocotyl, hldn2; Exp:Red; Ref: Green (Cy5:Cy3) Hypocotyl light vs Cultured cell : - Hypocotyl light, hln1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl light, hln2; Exp:Green; Ref: Red (Cy3:Cy5) Petal vs Cultured cell : - Petal, pn1; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn2; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn3; Exp:Green; Ref: Red (Cy3:Cy5) 1DBP vs Cultured cell : - Pistil 1DBP, pin1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin3; Exp:Green; Ref: Red (Cy3:Cy5) Pistil 1DPP vs Cultured cell : - Pistil 1DPP, psn1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn3; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn4; Exp:Green; Ref: Red (Cy3:Cy5) Root dark vs Cultured cell : - Root dark, rdn1; Exp:Green; Ref: Red (Cy3:Cy5) - Root dark, rdn2; Exp:Green; Ref: Red (Cy3:Cy5) Root light vs Cultured cell : - Root light, rln1; Exp:Green; Ref: Red (Cy3:Cy5) - Root light, rlp1; Exp:Red; Ref: Green (Cy5:Cy3) Root light vs Root dark : - Root light vs dark, rldp1; Exp:Red; Ref: Green (Cy5:Cy3) - Root light vs dark, rldp2; Exp:Red; Ref: Green (Cy5:Cy3) Rosette leaf vs Cultured cell : - Rosette leaf, rfp1; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp2; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp3; Exp:Red; Ref: Green (Cy5:Cy3) Sepal vs Cultured cell : - Sepal, sn1; Exp:Green; Ref: Red (Cy3:Cy5) - Sepal, sn2; Exp:Green; Ref: Red (Cy3:Cy5) Silique 3DPP vs Cultured cell : - Silique 3DPP, s3n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n3; Exp:Green; Ref: Red (Cy3:Cy5) Silique 8DPP vs Cultured cell : - Silique 8DPP, s8n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n3; Exp:Green; Ref: Red (Cy3:Cy5) Stamen vs Cultured cell : - Stamen, smn1; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn2; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl dark vs Cultured cell : - Hypocotyl dark, hn1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl dark, hn2; Exp:Green; Ref: Red (Cy3:Cy5) Stem vs Cultured cell : - Stem, stp1; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp2; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp3; Exp:Red; Ref: Green (Cy5:Cy3) Keywords: other

Dataset Information

Gene array analysis of human CD34+ hematopoietic cells exposed during 24h to HOXB4 or HOXC4 homeoproteins

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