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Transcription profiling of cell cycle in HeLa S3, mitotic selection, experiment 1

ABSTRACT: HeLa S3 cells in mitosis were selected by mitotic shake-off using an automated cell shaker (Eliassen et al. 2000, MCB)by Beth Alexander and Myra Hurt at Florida State University. This experiment set contains the complete set of 43K arrays for the first mitotic shake-off experiment described in Whitfield et al.(2002), (Shake).

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-905 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

Whitfield Michael L ML Sherlock Gavin G Saldanha Alok J AJ Murray John I JI Ball Catherine A CA Alexander Karen E KE Matese John C JC Perou Charles M CM Hurt Myra M MM Brown Patrick O PO Botstein David D

Molecular biology of the cell 20020601 6

The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic variation during the cell cycle. Hierarchical clustering of the expression patterns revealed coexpressed groups of previously well-characterized genes involved in essential cell cycle processes such as DNA replication, chromosome segregation, and cell adhesion along with genes of uncharacterized function. ...[more]

PMID: 12058064

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Cell division cycle in a human cancer cell line (HeLa)

Project description:This experiment set contains the complete set of raw data for Whitfield et al. (2002)Mol.Biol.Cell. HeLa S3 cells were synchronized by three different methods (double thymidine block, thymidine-nocodazole block or mitotic shake-off)in five independent time courses. mRNA from the first and second double thymidine block experiments were converted to cDNA by standard methods using an oligo-dT/random hexamer mix and hybridized to 24K arrays; mRNA from the third double thymidine and thymidine-nocodazole block experiments were converted to cDNA using olido-dT alone and hybridized to 43K arrays; total RNA from the mitotic shake-off experiment was first amplified using a modified eberwine protocol, aRNA converted to cDNA by reverse transcription with random hexamer and hybridized to 43K arrays. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-10-22 | GSE3497 | GEO

Cell division cycle in a human cancer cell line (HeLa)

2005-10-22 | E-GEOD-3497 | biostudies-arrayexpress

Transcription profiling of cell cycle in HeLa S3 cells, double thymidine block, experiment 3

Project description:HeLa S3 cells were synchronized in early S phase with a double thymidine block as described in Whitfield et al(2002)Mol.Biol.Cell. This experiment set contains the complete set of 43K arrays for the third double thymidine block synchronization (Thy-Thy3).

2005-09-22 | E-SMDB-903 | biostudies-arrayexpress

Transcription profiling of cell cycle in HeLa S3 cells, thymidine-nocodazole lock

Project description:HeLa S3 cells were synchronized in mitosis by arresting first in S phase with thymidine followed by arrest in mitosis with Nocodazole as described in Whitfield et al(2002)Mol.Biol.Cell. This experiment set contains the complete set of 43K arrays for the thymidine-nocodazole synchronization (Thy-Noc).

2005-09-22 | E-SMDB-904 | biostudies-arrayexpress

Hela Mitotic Selection - gene expression time series in early G1 phase of the human cell cycle

Project description:HeLa mitotic cells were collected using a mitotic shakeoff apparatus to study gene expression in early G1 phase of the human cell cycle. This set includes microarray data from two shake-off experiments : shake 1 (0h-14h) which was conducted over 14 hours and RNA samples collected every 2 hrs, and shake 2 (0min-120min) which was conducted over 2 hours and samples collected every 15 minutes. Total RNA was prepared using ULTRASPEC RNA isolation system, and Reference RNA was extracted from asynchronously growing HeLa cells using TRIzol. For cDNA synthesis and microarray hybridization, refer to Whitfield ML. et al., Mol Biol Cell, 2002. 13(6): p. 1977-2000. Groups of assays that are related as part of a time series. Age: g1 progression after mitotic shake-off Replicate: two biological replicates (shake1 and shake2) Keywords: time_series_design

2009-02-26 | GSE12473 | GEO

Hela Mitotic Selection - gene expression time series in early G1 phase of the human cell cycle

2010-06-25 | E-GEOD-12473 | biostudies-arrayexpress

Transcription profiling of cell cycle in HeLa S3 cells, double thymidine block, rxperiment 2

Project description:HeLa S3 cells were synchronized in early S phase with a double thymidine block as described in Whitfield et al(2002)Mol.Biol.Cell. This experiment set contains the complete set of 24K arrays for the second double thymidine block synchronization (Thy-Thy2).

2005-09-22 | E-SMDB-902 | biostudies-arrayexpress

Transcription profiling of cell cycle in HeLa S3 cells, double thymidine Block, experiment 1

Project description:HeLa S3 cells were synchronized in early S phase with a double thymidine block as described in Whitfield et al(2002)Mol.Biol.Cell. This experiment set contains the complete set of 24K arrays for the first double thymidine block synchronization (Thy-Thy1).

2005-09-22 | E-SMDB-901 | biostudies-arrayexpress

Mitotic chromosome binding predicts transcription factor properties in interphase [ATAC-Seq]

Project description:Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/ non-specific DNA binding affinity. How these properties affect the ability of TFs to occupy their specific binding sites in the genome and modify the epigenetic landscape is unclear. Here we combined live cell quantitative measurements of mitotic chromosome binding (MCB) of 502 TFs, measurements of TF mobility by fluorescence recovery after photobleaching, single molecule imaging of DNA binding in live cells, and genome-wide mapping of TF binding and chromatin accessibility. MCB scaled with interphase properties such as association with DNA-rich compartments, mobility, as well as large differences in genome-wide specific site occupancy that correlated with TF impact on chromatin accessibility. As MCB is largely mediated by electrostatic, non-specific TF-DNA interactions, our data suggests that non-specific DNA binding of TFs enhances their search for specific sites and thereby their impact on the accessible chromatin landscape.

2019-01-25 | GSE119781 | GEO

Mitotic chromosome binding predicts transcription factor properties in interphase [ChIP-Seq]

2019-01-25 | GSE119782 | GEO

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