Similar studies for GEO DataSets (Select 200025994) - GEO DataSets

Select item 2000259941.

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

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Series

Accession:: GSE25994

ID:: 200025994

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Select item 2000066772.

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

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Series

Accession:: GSE6677

ID:: 200006677

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Select item 2000086123.

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

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Series

Accession:: GSE8612

ID:: 200008612

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Select item 2000055184.

Differential gene expression of Appresorium vs Vegetative mycelium of Magnaporthe using oligoarray

(Submitter supplied) Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using MPSS, RL-SAGE and oligoarray methods. more...

Organism:: Pyricularia grisea

Type:: Expression profiling by array; Expression profiling by SAGE

Platforms:: GPL4080 GPL4085
2 Samples

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Series

Accession:: GSE5518

ID:: 200005518

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Select item 2000143135.

Gene expression profiling via LongSAGE in a non-model plant species: A case study in seeds of Brassica napus

(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. more...

Organism:: Brassica napus

Type:: Expression profiling by SAGE

Platform:: GPL8033
2 Samples

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Series

Accession:: GSE14313

ID:: 200014313

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Select item 2000029676.

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

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Series

Accession:: GSE2967

ID:: 200002967

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Select item 2000247887.

Digital gene expression profiling for maize development - 2mm ear libraries, B73 vs. ramosa3 mutant

(Submitter supplied) Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression (DGE) profiles using Illumina’s high-throughput sequencing technology and the newly-assembled B73 maize reference genome. more...

Organism:: Zea mays

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9141
7 Samples

Download data: GFF3, TXT

Series

Accession:: GSE24788

ID:: 200024788

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Select item 2000128328.

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

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Series

Accession:: GSE12832

ID:: 200012832

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Select item 2000293699.

Application of Serial Analysis of Gene Expression to the study of the gene expression profile of Leishmania infantum chagasi promastigote

(Submitter supplied) This study describes the application of the LongSAGE methodology to study the gene expression profile in Leishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. more...