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Expression and differential expression analysis of HFF cells in G0 phase compared to cells in G1 using nONCOchip 2.0 array

ABSTRACT: Expression and differential expression analysis of long non-coding RNAs and protein-coding genes. HFF cells were synchronised by serum starvation and reside in G0 phase or G1 phase of mitotic cell cycle.

ORGANISM(S): Homo sapiens

PROVIDER: GSE61006 | GEO | 2015/01/23

SECONDARY ACCESSION(S): PRJNA260079

REPOSITORIES: GEO

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Expression and differential expression analysis of HFF cells in G0 phase compared to cells in G1 using nONCOchip 2.0 array

Project description:Expression and differential expression analysis of long non-coding RNAs and protein-coding genes. HFF cells were synchronised by serum starvation and reside in G0 phase or G1 phase of mitotic cell cycle. We analyzed three arrays each for HFF cells in G0 phase and cells in G1 phase

2015-01-23 | E-GEOD-61006 | biostudies-arrayexpress

Expression and differential expression analysis of HFF cells in G0 phase compared to cells in G1

Project description:Expression and differential expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. HFF cells were synchronised by serum starvation and reside in G0 phase or G1 phase of mitotic cell cycle. We analyzed three arrays each for HFF cells in G0 phase and cells in G1 phase

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Project description:Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with Tiling Array Software (TAS). We analyzed one Affymetrix Human Tiling 1.0R set each for HFF cells in G0 phase and cells in G1 phase

2012-12-18 | E-GEOD-36160 | biostudies-arrayexpress

Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TileShuffle]

Project description:Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with our new permutation approach TileShuffle variant B. We analyzed one Affymetrix Human Tiling 1.0R set each for HFF cells in G0 phase and cells in G1 phase

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Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TAS]

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Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TileShuffle]

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Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [MAT]

Project description:Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). We analyzed one Affymetrix Human Tiling 1.0R set each for HFF cells in G0 phase and cells in G1 phase

2012-12-18 | E-GEOD-36156 | biostudies-arrayexpress

Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [MAT]

Project description:Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).

2012-12-18 | GSE36156 | GEO

Expression analysis of HFF cells in G0 phase [TileShuffle]

Project description:Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G0 phase. Expression data were processed with our new permutation approach TileShuffle.

2012-12-18 | GSE36162 | GEO

Expression and differential expression analysis of HFF cells in G0 phase compared to cells in G1

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