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Links from GEO DataSets

Items: 20

1.

A SAGE approach to discovery of apolipoprotein E4 allele-specific genes involved in increased risk in Alzheimer disease

(Submitter supplied) APOE4 allele is a major risk factor for late-onset Alzheimer disease (AD). The mechanism of action of APOE in AD remains unclear. To study the effects of APOE alleles on gene expression in AD, we have analyzed the gene transcription patterns of human hippocampus from APOE3/3, APOE3/4, APOE4/4 AD patients and normal control using Serial Analysis of Gene Expression (SAGE). Using SAGE, we found gene expression patterns in hippocampus of APOE3/4 and APOE4/4 AD patients differ substantially from those of APOE3/3 AD patients. more...
Organism:
Homo sapiens
Type:
Expression profiling by SAGE
Platforms:
GPL4 GPL1485
6 Samples
Download data
Series
Accession:
GSE6677
ID:
200006677
2.

SAGE and MPSS libraries from activated CD4+ T cell clone 29

(Submitter supplied) SAGE and MPSS libraries were produced from the same RNA sample extracted from an activated CD4+ T cell clone in order to compare the ability of these techniques to indentify the full range of genes expressed in a single cell type. Keywords: Technical comparison of tag-based technologies SAGE and MPSS
Organism:
Homo sapiens
Type:
Expression profiling by SAGE; Expression profiling by MPSS
Platforms:
GPL5678 GPL5624
4 Samples
Download data: TXT
Series
Accession:
GSE8612
ID:
200008612
3.

Comparative molecular analysis of developing mouse forelimbs and hindlimbs

(Submitter supplied) The analysis of differentially expressed genes is a powerful approach to elucidate the genetic mechanisms underlying the morphological and evolutionary diversity among serially homologous structures, both within the same organism (e.g., hand vs. foot) and between different species (e.g., hand vs. wing). In the developing embryo, limb-specific expression of Pitx1, Tbx4, and Tbx5 regulates the determination of limb identity. more...
Organism:
Mus musculus
Type:
Expression profiling by SAGE
Platform:
GPL11
2 Samples
Download data
Series
Accession:
GSE504
ID:
200000504
4.

RL-SAGE analysis of Zea mays leaf transcriptome

(Submitter supplied) Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library.
Organism:
Zea mays
Type:
Expression profiling by SAGE
Platform:
GPL1462
1 Sample
Download data
Series
Accession:
GSE25994
ID:
200025994
5.

LongSAGE analysis significantly improves genome annotation

(Submitter supplied) Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS: A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. more...
Organism:
Mus musculus
Type:
Expression profiling by SAGE
Platform:
GPL1349
1 Sample
Download data
Series
Accession:
GSE2967
ID:
200002967
6.

APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer's Disease Phenotypes in Human iPSC-Derived Brain Cell Types

(Submitter supplied) The apolipoprotein E4 (APOE4) variant is the single greatest genetic risk factor for sporadic Alzheimer's disease (sAD). However, the cell-type-specific functions of APOE4 in relation to AD pathology remain understudied. Here, we utilize CRISPR/Cas9 and induced pluripotent stem cells (iPSCs) to examine APOE4 effects on human brain cell types. Transcriptional profiling identified hundreds of differentially expressed genes in each cell type, with the most affected involving synaptic function (neurons), lipid metabolism (astrocytes), and immune response (microglia-like cells). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL18573 GPL11154
26 Samples
Download data: TXT
Series
Accession:
GSE102956
ID:
200102956
7.

SAGE tags generated from Triticum aestivum cultivars Scorpion 25 and Xi19 grown under normal and hot/dry conditions

(Submitter supplied) Triticum aestivum cultivars Scorpion 25 and Xi 19 were grown under both normal and hot/dry conditions. We compared the effect of these two growth conditions on these two closely related varieties.
Organism:
Triticum aestivum
Type:
Expression profiling by SAGE
Platform:
GPL7079
6 Samples
Download data
Series
Accession:
GSE12832
ID:
200012832
8.

Adult mouse testis

(Submitter supplied) SAGE libraries generated from total testes of adult mouse males. Keywords = testis Keywords: other
Organism:
Mus musculus
Type:
Expression profiling by SAGE
Platform:
GPL11
2 Samples
Download data
Series
Accession:
GSE1939
ID:
200001939
9.

The pattern of gene expression in human CD34(+) stem/progenitor cells

(Submitter supplied) We have analyzed the pattern of gene expression in human primary CD34(+) stem/progenitor cells. We identified 42,399 unique serial analysis of gene expression (SAGE) tags among 106,021 SAGE tags collected from 2.5 x 10(6) CD34(+) cells purified from bone marrow. Of these unique SAGE tags, 21,546 matched known expressed sequences, including 3,687 known genes, and 20,854 were novel without a match. The SAGE tags that matched known sequences tended to be at higher levels, whereas the novel SAGE tags tended to be at lower levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by SAGE
Platform:
GPL4
1 Sample
Download data
Series
Accession:
GSE2346
ID:
200002346
10.

Sperm storage mechanisms in poultry

(Submitter supplied) Turkey sperm lose viability within 8-18 h when stored as liquid semen using current methods and extenders. In contrast, turkey hens maintain viable, fertile sperm in their sperm storage tubules (SST) for 45 or more days following a single insemination. Our long-term objectives are to identify and characterize differentially expressed genes that may underlie this prolonged sperm storage and then use this information to develop improved methods for storing liquid turkey semen. more...
Organism:
Meleagris gallopavo
Type:
Expression profiling by SAGE
Platform:
GPL279
2 Samples
Download data
Series
Accession:
GSE351
ID:
200000351
11.

Bombyx mori Posterior and Median Silk Gland SAGE transcriptome

(Submitter supplied) To identify functions that distinguish the posterior and median cells producing fibroin and sericin in the silk gland of Bombyx mori, serial analysis of gene expression (SAGE) profiles from both silk gland regions were analyzed and compared. The construction of a B. mori reference tag collection extracted from a set of 38000 Bombyx EST sequenced from the 3’ side, helped annotating the SAGE libraries. more...
Organism:
Bombyx mori
Type:
Expression profiling by SAGE
Platform:
GPL2095
2 Samples
Download data
Series
Accession:
GSE23098
ID:
200023098
12.

Evaluation of the chicken transcriptome by SAGE of B cell and the DT40 cell line

(Submitter supplied) These libraries represent total RNA from bursal tissue of 20 day old CB-inbred chicks and the ALV induced bursal cell line DT40 Cre1 cells. Keywords = chicken transcriptome SAGE Bursal cell DT40 Keywords: other
Organism:
Gallus gallus
Type:
Expression profiling by SAGE
Platform:
GPL1477
2 Samples
Download data
Series
Accession:
GSE1817
ID:
200001817
13.

Bovine Glomerular and Aortic Endothelial Cells

(Submitter supplied) SAGE libraries were prepared from mRNA of cultured bovine glomerular and aortic endothelial cells. Cells both cell lines were positive for acetylated LDL uptake and vWF expression, and were proven to be free of non-endothelial cells. Cultures were studied at passage 9-10. The cells were confluent, cultured in parallel, under identical conditions. Cells were plated on gelatin coated cell culture plastic in RPMI 1640 medium containing 10% FBS and streptomycin/penicillin. more...
Organism:
Bos taurus
Type:
Expression profiling by SAGE
Platform:
GPL223
2 Samples
Download data
Series
Accession:
GSE110
ID:
200000110
14.

Wilms tumor versus Stratagene Universal Reference

(Submitter supplied) Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA Keywords: repeat sample
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS1791
Platform:
GPL96
4 Samples
Download data
Series
Accession:
GSE1158
ID:
200001158
15.
Full record GDS1791

Wilms' tumor

Expression profiling of Wilms' tumor tissue after pre-operative chemotherapy. Stratagene Universal Reference RNA also examined. Results are part of a cross-platform evaluation and compared to data generated from Serial Analysis of Gene Expression.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 2 other sets
Platform:
GPL96
Series:
GSE1158
4 Samples
Download data
16.

Serial analysis of gene expression in the corneal endothelium of Fuchs' dystrophy

(Submitter supplied) PURPOSE: To compare the gene expression profiles of normal human corneal endothelium with Fuchs' corneal endothelium, by using serial analysis of gene expression (SAGE). METHODS: Three pairs of normal human corneas were obtained from eye banks. Thirteen bisected Fuchs' corneal buttons were processed at the time of corneal transplantation. The endothelia of normal and Fuchs'-affected corneas were stripped, and total RNA was isolated. more...
Organism:
Homo sapiens
Type:
Expression profiling by SAGE
Platform:
GPL4
2 Samples
Download data
Series
Accession:
GSE505
ID:
200000505
17.

SAGE analysis of A. thaliana leaf tissue

(Submitter supplied) Arabidopsis thaliana (Col-4) aerial tissue collected from 14-day old plants. Grown under sterile conditions at 22 degrees Celsius and 125 uE light on 0.5xMS media.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by SAGE
Platform:
GPL25
1 Sample
Download data
Series
Accession:
GSE25993
ID:
200025993
18.

LongSAGE transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

(Submitter supplied) The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. more...
Organism:
Emiliania huxleyi CCMP1516
Type:
Expression profiling by SAGE
Platform:
GPL5469
3 Samples
Download data
Series
Accession:
GSE8376
ID:
200008376
19.

LSAGE Library Human Renal Glomeruli

(Submitter supplied) Glomeruli were isolated from the kidney of a 72 yo male patient. The kidney was surgically removed due to renal cell carcinoma. The glomeruli were isolated from uninvolved renal parenchyma. Histology (H&E) of glomeruli and interstitium was normal. Keywords: Kidney Subcompartment
Organism:
Homo sapiens
Type:
Expression profiling by SAGE
Platform:
GPL1485
1 Sample
Download data
Series
Accession:
GSE8114
ID:
200008114
20.

Incipient Alzheimer's Disease: Microarray Correlation Analyses

(Submitter supplied) For these data, we analyzed hippocampal gene expression of nine control and 22 AD subjects of varying severity on 31 separate microarrays. We then tested the correlation of each gene's expression with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores across all 31 subjects regardless of diagnosis. These tests revealed a major transcriptional response comprising thousands of genes significantly correlated with AD markers. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS810
Platform:
GPL96
31 Samples
Download data: CEL, EXP, RPT, TXT
Series
Accession:
GSE1297
ID:
200001297
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