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GSE18679
Homo sapiens
5 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The organization of mammalian DNA replication is poorly understood. We have produced genome-wide high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal and embryonic stem cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy number variations during S phase obtained using either high-density oligonucleotide tiling arrays or massively-parallel sequencing to produce replication timing profiles. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by SMARD analysis. Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarter of S phase and that ES cells replicate a larger proportion of their genome in early S phase than erythroid cells. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid firing origins are located near moderately expressed genes and that late firing origins are located far from genes.
Publication Title
Predictable dynamic program of timing of DNA replication in human cells.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 99 Downloadable Samples
IlluminaHiSeq2000, IlluminaHiScanSQ
Description
The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR. Overall design: 105 samples were selected from the DrugMatirx tissue/RNA bank that is now owned by the National Toxicology Program (NTP). The samples were split into 2 sets, training and test, to allow for the evaluation of classifiers derived from the data. There were 63 samples in the training set and 42 in the test set. Of the 63 samples in the training set 45 were derived from rats treated with test agent and 18 were control samples (3 sets of 6). 39 of the test set samples were derived from test agent treated animals and 6 were from vehicle and route matched controls. Five MOAs were represented in the training set and 4 MOAs were in the test set. Two of the MOAs were duplicated from the test set and two were without representation in the training set. For each test agent there were three rats treated, in accordance with the common practice in the field of toxicology. For each MOA there were three representative test agents to ensure adequate power for detecting the MOA signatures. 6 samples from the training set had duplicate libraries sequenced and duplicate sequencing runs for the first library. DrugMatrix, National Toxicology program (NTP) Sequencing was carried out in Dr. Charles Wang's Functional Genomics Core at City of Hope Comprehensive Cancer Center, Duarte, CA
Publication Title
Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Interleukin-21 (IL-21) is a pleiotropic cytokine that induces expression of transcription factor BLIMP1 (encoded by Prdm1), which regulates plasma cell differentiation and T cell homeostasis. We identified an IL-21 response element downstream of Prdm1 that binds the transcription factors STAT3 and IRF4, which are required for optimal Prdm1 expression. Genome-wide ChIP-Seq mapping of STAT3- and IRF4-binding sites showed that most regions with IL-21-induced STAT3 binding also bound IRF4 in vivo, and furthermore, revealed that the noncanonical TTCnnnTAA GAS motif critical in Prdm1 was broadly used for STAT3 binding. Comparing genome-wide expression array data to binding sites revealed that most IL-21-regulated genes were associated with combined STAT3-IRF4 sites rather than pure STAT3 sites. Correspondingly, ChIP-Seq analysis of Irf4_/_ T cells showed greatly diminished STAT3 binding after IL-21 treatment, and Irf4_/_ mice showed impaired IL- 21-induced Tfh cell differentiation in vivo. These results reveal broad cooperative gene regulation by STAT3 and IRF4.
Publication Title
Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 transcription factors.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 170 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Chemo-resistance to platinum such as cisplatin is critical in the treatment of ovarian cancer. Recent evidences have linked epithelial-mesenchymal transition (EMT) with the drug resistance as a contributing mechanism. The current study explored the connection between cellular responses to cisplatin with EMT in ovarian cancer.
Publication Title
Epithelial-mesenchymal status renders differential responses to cisplatin in ovarian cancer.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
For more than a decade, microarrays have been a powerful and widely used tool to explore the transcriptome of biological systems. However, the amount of biological material from cell sorting or laser capture microdissection is much too small to perform microarray studies. To address this issue, RNA amplification methods have been developed to generate sufficient targets from picogram amounts of total RNA to perform microarray hybridisation. In this study, four commercial protocols for amplification of picograms amounts of input RNA for microarray expression profiling were evaluated and compared. The quantitative and qualitative performances of the methods were assessed. Microarrays were hybridised with the amplified targets and the amplification protocols were compared with respect to the quality of expression profiles, reproducibility within a concentration range of input RNA, and sensitivity.
Publication Title
Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 425 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The purpose of this study is to obtain comprehensive gene expression profiles in breast cancer. Mammary gland cells were specifically isolated from 433 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 417 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip.
Publication Title
Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 99 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
A collection of 100 ovarian cancer sample gene expression data from Singapore.
Publication Title
CSIOVDB: a microarray gene expression database of epithelial ovarian cancer subtype.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Neuroprotective therapies for retinal degeneration may be used to rescue retinal cells and preserve vision. Hypoxic preconditioning stabilizes the transcription factor HIF-1 in the retina and strongly protects photoreceptors in an animal model of light-induced retinal degeneration.
Publication Title
Analysis of the retinal gene expression profile after hypoxic preconditioning identifies candidate genes for neuroprotection.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 21 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
Modulation of several waves of gene expression during FGF-1 induced Epithelial-mesenchymal transition of carcinoma cells . In vitro FGF-1 induced EMT study using NBTII rat bladder carcinoma cells
Publication Title
Modulation of several waves of gene expression during FGF-1 induced epithelial-mesenchymal transition of carcinoma cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 55 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Ovarian cancer is characterized by multiple structural aberrations; most are passenger alterations which do not confer tumor growth. Like many cancers, it is a heterogeneous disease and till date, the histotype-specific copy number landscape has been difficult to elucidate. To dissect the heterogeneity of ovarian cancer and understand the pathogenesis of its various histotypes, we developed an in silico hypothesis-driven workflow to identify histotype-specific copy number aberrations across multiple datasets of epithelial ovarian cancer. In concordance with previous studies on global copy number changes, our study showed similar alterations. However, when the landscape was de-convoluted into histotypes, distinct alterations were observed. We report here a comprehensive histotype-specific copy number landscape of ovarian cancer and showed that there is genomic diversity between the histotypes; some involving well known cancer genes and some novel potential driver genes. Besides preferential occurrence of alterations in some histotypes, opposite trends of alteration were observed; such as ERBB2 amplification in mucinous but deletion in serous tumors. The landscape highlights the need for identifying histotype-specific aberrations in ovarian cancer and present potential to tailor management of ovarian cancer based on molecular signature of histotypes.
Publication Title
Histotype-specific copy-number alterations in ovarian cancer.
Sample Metadata Fields
No sample metadata fields
View Samples