Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

SUBMITTER: Kristin Reiche

PROVIDER: E-GEOD-36164 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Project description:This SuperSeries is composed of the following subset Series: GSE36162: Expression analysis of HFF cells in G0 phase [TileShuffle] GSE36163: Expression analysis of HFF cells in G1 phase [TileShuffle] GSE36164: Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TileShuffle] Refer to individual Series

2012-06-05 | E-GEOD-36190 | biostudies-arrayexpress

Expression analysis of HFF cells in G1 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 G1 phase. Expression data were processed with our new permutation approach TileShuffle. We analyzed one Affymetrix Human Tiling 1.0R set

2012-12-18 | E-GEOD-36163 | biostudies-arrayexpress

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. We analyzed one Affymetrix Human Tiling 1.0R set

2012-12-18 | E-GEOD-36162 | biostudies-arrayexpress

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

Project description:This SuperSeries is composed of the following subset Series: GSE36154: Expression analysis of HFF cells in G0 phase [MAT] GSE36155: Expression analysis of HFF cells in G1 phase [MAT] GSE36156: Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [MAT] Refer to individual Series

2012-06-05 | E-GEOD-36187 | biostudies-arrayexpress

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

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 [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

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

2012-06-05 | E-GEOD-29792 | biostudies-arrayexpress

Expression analysis of HFF cells in G1 phase using TAS

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 G1 phase. Expression data were processed with Tiling Array Software (TAS). We analyzed one Affymetrix Human Tiling 1.0R set

2012-12-18 | E-GEOD-29834 | biostudies-arrayexpress

Expression analysis of HFF cells in G0 phase using TAS

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 Tiling Array Software (TAS). We analyzed one Affymetrix Human Tiling 1.0R set

2012-12-18 | E-GEOD-29833 | biostudies-arrayexpress

RNA-sequencing based analysis of Listeria monocytogenes 10403S::ÎBCHL Prha-sigH and ÎBCHL Prha

Project description:In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::ÎBCHL Prha-sigH and ÎBCHL Prha. RNA-seq was performed on ÎBCHL Prha-sigH and ÎBCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains was statistically assessed using the BaySeq method. To identify sigH-dependent promoters, a new method of moving sliding windows of 50 nt along the whole genome was used to compare the normalized RNA-seq coverage (NRC) between the two strains. Using the standard whole gene differential expression analysis, significant upregulation of 5 genes in 4 operons was found in the sigH overexpressing strain. While with the sliding windiow analysis, 2 additional ÏH-dependent promoters were identified. Our results show that three ÏH-dependent transcritption units that encode competence proteins, including the comEABC , comGABCDEFG and coiA. Transcriptome profiles of L. monocytogenes 10403S::ÎBCHL Prha-sigH and ÎBCHL Prha were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

2016-02-11 | E-GEOD-73008 | 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