GEO DataSets

(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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(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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(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

(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

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(Submitter supplied) Gene expression profiling of zebrafish early eye development on 3 to 5 days post fertilization (dpf)

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

9 Samples

Download data: CEL

(Submitter supplied) Mouse Atlas of Gene Expression Project A Quantitative and Comprehensive Atlas of Gene Expression in Mouse Development. Also available at CGAP: http://cgap.nci.nih.gov/ Keywords: LongSAGE, SAGE

Organism:

Mus musculus

Type:

Expression profiling by SAGE

Platforms:

GPL1349 GPL11

203 Samples

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(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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(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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(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...

Organism:

Leishmania chagasi

Type:

Expression profiling by SAGE

Platform:

GPL11414

1 Sample

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(Submitter supplied) We performed strand-specific, deep RNA sequencing to profile expression of sense and antisense reads with a focus on 100 ASD-related genes in medial prefrontal cortex (mPFC) and striatum across mouse development (P7, P14 and P56). Using de novo transcriptome assembly, we generated a comprehensive long non-coding RNA (lncRNA) transcriptome. We conducted BLAST analyses to compare the resultant transcripts with the human genome and identified transcripts with high sequence similarity and coverage.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: GTF, MTX

(Submitter supplied) Gene expression profiles before and after spore formation of Lentinula edodes (L54) grown at sawdust.

Organism:

Lentinula edodes

Type:

Expression profiling by SAGE

Platform:

GPL11229

2 Samples

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(Submitter supplied) spotted cDNA

Organism:

Mus musculus

1 Series

92 Samples

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(Submitter supplied) spotted cDNA

Organism:

Mus musculus

1 Series

106 Samples

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(Submitter supplied) spotted cDNA

Organism:

Mus musculus

1 Series

58 Samples

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(Submitter supplied) Comparison of sense (forward probes) and antisense (reverse probes on U74 v1 gene arrays) transcripts in mouse kidney and brain. Positive calls related to antisense transcripts were compared to the cognate signals on the 430 version of mouse genome arrays to obtain genes that co expressed sense and antisense transcripts. This had to be done manually because divergent probe IDs on the two chip generations. more...

Organism:

Mus musculus

Type:

Expression profiling by array

5 related Platforms

7 Samples

Download data: CEL

(Submitter supplied) Sense-antisense transcript (SAT) pairs are pairs of transcripts that fully or partially overlap but are transcribed in opposite directions. Although SAT expression occurs in various species, most SAT pairs have not been examined in detail. Because our previous studies revealed some tissue specificity in SAT expression, SAT pairs might be involved in cell differentiation and the maintenance of tissue-specific gene expression programs. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL8064 GPL8065

47 Samples

Download data: TXT

(Submitter supplied) In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . more...

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23263

28 Samples

Download data: TXT

(Submitter supplied) Background: A comprehensive transcriptome survey, or "gene atlas", provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and 3 cattle cell lines. Results: The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the bovine genome accounting for 85% of the total raw tag abundance. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9323

95 Samples

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