| Summary: | (Submitter supplied) Mantle cell lymphoma is characterized by a t(11;14) chromosomal translocation; however, it alone is insufficient to result in the disease. A number of secondary genetic alterations have been proposed as essential in MCL pathogenesis. Amongst these, numerous copy number altered regions remain ill-defined, both for location and prognostic significance. In this study we examined in detail the genomes of a panel of 52 MCL cases. Relating gene dosage alterations to disease outcome, we found seven loci that correlated with overall survival. A survival model was constructed based on four of these loci (P = 5.87 x 10-6). Using serial analysis of gene expression and quantitative PCR we investigated the expression of genes within these altered regions and determined that CCNI and CCNG2 may be important in MCL pathogenesis (P = 0.0201 and P = 0.0292, respectively). more...
3 related Platforms
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| Type: | Expression profiling by SAGE; Genome variation profiling by array; Genome variation profiling by genome tiling array |
| Supplementary Files: | TXT download... |
| Samples: | 57 |
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| Summary: | (Submitter supplied) Background: The development and maintenance of the prostate is dependent on androgens and the androgen receptor. The androgen pathway continues to be important in prostate cancer. Here, we evaluated the transcriptome of prostate cancer cells in response to androgen using long serial analysis of gene expression (LongSAGE) libraries. Results: There were 131 tags (87 genes) that displayed statistically significant (p=<0.001) differences in expression in response to androgen. Many of the genes identified by LongSAGE (35/87) have not been previously reported to change expression in the direction or sense observed. In regulatory regions of the promoter and/or enhancer regions of some of these genes there are confirmed or potential androgen response elements (AREs). The expression trends of 24 novel genes were validated using quantitative real time-polymerase chain reaction (qRT-PCR). more...
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 2 |
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| Summary: | (Submitter supplied) This SuperSeries is composed of the following subset Series: GSE11912: Comparison of TCF hyper-activated and control Huh7 cells - SAGE GSE11916: Comparison of TCF hyper-activated and control Huh7 cells - microarray data
2 related Platforms
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| Type: | Expression profiling by array; Expression profiling by SAGE |
| Supplementary Files: | CEL TAR download... |
| Samples: | 8 |
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| Summary: | (Submitter supplied) The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. Β-catenin, a cytoplasmic component, plays a major role in the transduction of the canonical wnt/ β-catenin signaling. The aim of this study was to identify novel genes that are regulated by active β-catenin/TCF signaling in hepatocellular carcinoma. We selected and expanded isogenic clones from hepatocellular carcinoma-derived Huh7 cells with high and low β-catenin/TCF activities. We showed that, high TCF activity Huh7 cells lead to bigger and more aggressive tumors when xenografted into nude mice. We used SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis in parallel, to compare gene expression between low (basal) and high (transfected) β-catenin/TCF activity clones, those had been xenografted into nude mice. more...
1 related Platform
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| Type: | Expression profiling by SAGE |
| Supplementary Files: | TAR download... |
| Samples: | 2 |
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| Summary: | (Submitter supplied) The cerebral cortex plays an important role in cognitive function and specialized perception in mammals and its development requires highly specific spatio-temporal control of gene expression. The study identified stage- and region-specific markers throughout cerebral corticogenesis at various important stages of cerebral cortex development; embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4-6 months old.
2 related Platforms
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| Type: | Expression profiling by SAGE |
| Samples: | 12 |
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| Summary: | (Submitter supplied) Hürthle cells are found in thyroid tumors and autoimmunity, and have a unique appearance characterized by swollen eosinophilic cytoplasm filled with mitochondria and hyperchromatic nucleus. The pathogenesis of Hürthle cells remains unknown. We have generated transgenic mice expressing IFNg specifically in thyroid gland, and shown they develop changes in the thyroid follicular cell that resemble those of the human Hürthle cell. Transcriptome analysis by serial analysis of gene expression revealed an increased expression of immunoproteasome subunits in transgenic thyrocytes. LMP2, an immunoproteasome subunit also known as PSMB9 or ib1, provided critical for Hürthle cells and hypothyroidism development. Transgenic mice treated with a proteasome inhibitor ameliorated the Hürthle cell phenotype, and failed to develop it when crossed to LMP2 deficient mice. more...
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 2 |
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| Summary: | (Submitter supplied) The late blight pathogen, Phytophthora infestans has a broad host range within the Solanaceae family, including yellow potato (Solanum phureja). The disease caused by P. infestans in S. phureja is poorly understood and is a major concern in Colombia. Expressed Sequence Tag (EST) libraries obtained from a normalized library constructed from healthy plant tissue revealed high levels of sequence similarity between S. phureja and S. tuberosum. Then, utilizing Serial Analysis of Gene Expression and high-throughput sequencing (SAGE-Solexa), we characterized yellow potato gene expression during infection by P. infestans. Four-week-old yellow potato plants were inoculated with P. infestans and were collected at 12 and 72 hours post inoculation for RNA extraction. We detected differentially expressed genes by comparing inoculated to non-inoculated and resistant to susceptible plants. more...
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 6 |
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| Summary: | (Submitter supplied) A transcriptome study in mouse hematopoietic stem cells was performed using a sensitive SAGE method, in an attempt to detect medium and low abundant transcripts expressed in these cells. Among a total of 31,380 unique transcript, 17,326 (55%) known genes were detected, 14,054 (45%) low-copy transcripts that have no matches to currently known genes. 3,899 (23%) were alternatively spliced transcripts of the known genes and 3,754 (22%) represent anti-sense transcripts from known genes.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 1 |
| - GSM404329: Mus musculus hematopoietic stem cell
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| Summary: | (Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive fibrosing interstitial lung disease that is unresponsive to current therapy. While it carries a median survival of less than 3 years its rate of progression varies widely between patients. We hypothesized that studying the gene expression profiles of physiologically stable patients and those in which the disease progressed rapidly after the initial diagnosis would aid in the search for biomarkers and contribute to the understanding of disease pathogenesis.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 14 |
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| Summary: | (Submitter supplied) This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 280 |
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| Summary: | (Submitter supplied) This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 324 |
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| Summary: | (Submitter supplied) This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 34 |
| - GSM384523: mLSAGE_Embryo_normal_TS34_MMD_SM173
- GSM384652: mLSAGE_Vascular_endothelium_normal_muscle_associated_AP_NMEC1
- GSM384649: mLSAGE_Vascular_endothelium_normal_kidney_associated_AP_NKEC1
- GSM384646: mLSAGE_Vascular_endothelium_LLC_tumor_associated_AP_LLCTEC
- GSM384526: mLSAGE_Embryo_normal_TS7_MMD_SM106
- GSM384640: mLSAGE_Vascular_endothelium_24hr_regenerating_liver_associated_AP_24hrRLiEC
- GSM384643: mLSAGE_Vascular_endothelium_CT26_tumor_associated_AP_CT26TEC
- GSM384647: mLSAGE_Vascular_endothelium_normal_brain_associated_AP_NBEC1
- GSM384581: mLSAGE_MEF_normal_CL_SHE18
- GSM384521: mLSAGE_Embryo_normal_TS2_MMD_SM061
- GSM384632: mLSAGE_Urogenital_sinus_normal_TS18_MMD_SM065
- GSM384533: mLSAGE_Embryonic_stem_cells_normal_TS38_MMD_SM302
- GSM384642: mLSAGE_Vascular_endothelium_72hr_regenerating_liver_associated_AP_72hrRLiEC
- GSM384524: mLSAGE_Embryo_normal_TS34_MMD_SM211
- GSM384568: mLSAGE_Lung_normal_TS13_MMD_SM127
- GSM384570: mLSAGE_Lung_normal_TS19_MMD_SM045
- GSM384653: mLSAGE_Vascular_endothelium_normal_spleen_associated_AP_NSEC1
- GSM384650: mLSAGE_Vascular_endothelium_normal_liver_associated_AP_NLiEC1
- GSM384528: mLSAGE_Embryo_normal_TS7_MMD_SM204
- GSM384645: mLSAGE_Vascular_endothelium_KM12SM_tumor_associated_AP_KM12TEC
- GSM384482: mLSAGE_Brain_normal_P84-P90_MMD_SM201
- GSM384585: mLSAGE_Neural_tube_normal_TS9_MMD_SM117
- GSM384582: mLSAGE_Muscle_normal_TS19_MMD_SM042
- GSM384644: mLSAGE_Vascular_endothelium_EMT6_tumor_associated_AP_EMT6TEC
- GSM384641: mLSAGE_Vascular_endothelium_48hr_regenerating_liver_associated_AP_48hrRLiEC
- GSM384529: mLSAGE_Embryo_normal_TS7_MMD_SM205
- GSM384596: mLSAGE_Pancreas_normal_TS21_MMD_SM225
- GSM384567: mLSAGE_Lung_normal_P109_MMD_SM212
- GSM384654: mLSAGE_Vascular_endothelium_SW620_tumor_associated_AP_SW620TEC
- GSM384651: mLSAGE_Vascular_endothelium_normal_lung_associated_AP_NLgEC1
- GSM384551: mLSAGE_Kidney_normal_TS14_MMD_SM169
- GSM384548: mLSAGE_Heart_normal_TS9_MMD_SM174
- GSM384648: mLSAGE_Vascular_endothelium_normal_heart_associated_AP_NHEC1
- GSM384522: mLSAGE_Embryo_normal_TS34_MMD_SM146
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| Summary: | (Submitter supplied) This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 36 |
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| Summary: | (Submitter supplied) Biomphalaria glabrata infection by the Schistosoma mansoni free-swimming miracidium and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and triggers a variety of physiological, biochemical and molecular changes. Here, we describe a genome-wide analysis of the S. mansoni miracidium and developing sporocyst. Keywords: life-cycle, development, host-interaction
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 5 |
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| Summary: | (Submitter supplied) Babesia infected (and control) ovary tissue was used to construct LongSAGE libraries. The intent was to find differential gene expression in both libraries. Details: The extraction was done using Ambion's ToTALLY RNA kit, and the concatemers where constructed using Invitrogen's I-SAGE Long kit. The concatmer files (multiple fasta sequence files) were processed using in-house perl scripts to extract the 17bp LongSAGE tags. **Note: contact person: Felix D. Guerrero. email: felix.guerrero@ars.usda.gov Keywords: LongSAGE
1 related Platform
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| Type: | Expression profiling by SAGE |
| Supplementary Files: | TXT download... |
| Samples: | 2 |
| - GSM249490: Ovary control(time zero) B. microplus
- GSM249492: Ovary Babesia Infected (6 hours) B. microplus
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| Summary: | (Submitter supplied) Serial Analysis of Gene Expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression in about 10 % of all matched genes, with a total abundance of 44 %, showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. more...
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 2 |
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| Summary: | (Submitter supplied) In this study we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK), a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. As part of the same study we also analyzed the gene expression profiles by SAGE.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 2 |
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| Summary: | (Submitter supplied) We identified 3418 genes transcribed at a level of at least two copies each. We identified many transcripts involved in protein translation, cell maintenance and metabolism, as expected for vegetative cells. The most highly expressed cell signaling genes include ubiquitin, smlA, and nucleotide exchange factors RasGEF F and Ras GEF G. Additionally, we identified many genes previously reported to be expressed only during later stages of development including dutA, actin8, thioredoxin3, culmination specific protein 45D, discoidin II and yelA.
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 1 |
| - GSM304530: Dictyostelium discoideum amoeba stage SAGE library
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| Summary: | (Submitter supplied) Three SAGE libraries brushed from the surface of the tongue and three SAGE libraries extracted from oral biopsies define the normal oral transcriptome. Keywords: SAGE, normal oral
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 6 |
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| Summary: | (Submitter supplied) Recent improvements in the development of methods for isolating functionally validated populations of nearly pure (>20%) murine hematopoietic stem cells (HSCs) have made it possible to analyze the molecular basis of the properties of these cells with increased precision. One intriguing feature of HSCs is the change they undergo in many of their key properties during development a change that affects the control of their self-renewal, cycling status, differentiated progeny output and steel factor sensitivity. To investigate how these differences are mediated, we undertook a genome-wide analysis of the transcripts present in highly purified fetal and adult HSCs using an adaptation of the LongSAGE methodology that allows its application to small numbers of cells (10 ng of RNA) by inclusion of an initial PCR amplification step that preserves the transcript repertoire while excluding less than 0.25% of the transcripts. more...
1 related Platform
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| Type: | Expression profiling by SAGE |
| Samples: | 2 |
| - GSM333945: bone_marrow_hematopoietic_stem_cells
- GSM333946: fetal_liver_hematopoietic_stem_cells
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