GEO DataSets

(Submitter supplied) Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21493

3 Samples

Download data: BEDGRAPH

(Submitter supplied) Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21493

27 Samples

Download data: TXT

(Submitter supplied) H. pylori infection of human gastric epithelial cells (GEC) represses H,K-ATPase alpha subunit (HK-alpha) gene transcription through NF-Kappa B p50 homodimer binding to HK-alpha promoter. The bacterial cagA and slt gene products have been implicated in HK-alpha repression, which facilitates gastric H. pylori colonization and may underlie transient clinical hypochlorhydria. We hypothesized that H. pylori also regulates H,K-ATPase expression post-transcriptionally by micro-RNA interaction with HK-alpha mRNA. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

9 Samples

Download data: CEL

(Submitter supplied) Phloem is essential for higher plant development and survival by transporting photosynthetic products and systemic signals from source to sink organs. To date, most phloem studies were performed with the phloem exudate for physiological, transcriptomic or proteomic analyses. However, as yet, no transcriptomic profiling was performed to the phloem tissue itself, probably due to the technique difficulties to access the phloem tissue inside the plant body. more...

Organism:

Cucumis sativus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16310

6 Samples

Download data: TXT

(Submitter supplied) In this study, genome-wide transcriptome profiling was used to understand molecular genetic mechanism of drought tolerance in rice. Illumina High-Seq 2000 platform was used for sequencing RNA from leaf tissue of rice plants exposed to controlled drought stress and well-watered conditions. The differentially expressed genes were used to identify biological process and cis-regulatory elements enriched under drought stress compared to well-watered conditions.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19657

4 Samples

Download data: DIFF

(Submitter supplied) Background: Laryngeal squamous cell carcinoma (LSCC) is the most common type in head and neck squamous cell carcinoma (HNSCC), and the development of LSCC are multistep processes accompanied by changes of molecular biology. Objective: The purpose of this study was to investigate the miRNAs basis of tumorigenesis in LSCC, and analyze the microRNAs dysregulation related with the six targeted genes (CDK1,CDK2, CDK4, MCM2, MCM3, MCM4) which were related to tumorigenesis from the screened miRNAs. more...

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

10 Samples

Download data: CEL

(Submitter supplied) The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15520 GPL11154

22 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) MiRNA expression profiling on 14.5 day old testis from sterile (PWD x B6)F1, (PWK x B6)F1 and fertile (B6 x PWD)F1 inter-subspecific hybrids were performed to study the genome wide variation in miRNA expression between different inter-subspecific hybrids during meiosis.

Organism:

synthetic construct; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL8786

6 Samples

Download data: CEL

(Submitter supplied) Orchids are commercially important flowers, comprising one of the largest families of plants. Model plants such as Arabidopsis do not contain all plant genes. In this study, several molecular biology tools were integrated to isolate the flower-specific gene promoters of Oncidium Gower Ramsey (GR). A cDNA library of reproductive tissues was constructed and a microarray was established and used to compare gene expression in flowers and leaves. more...

Organism:

Oncidium hybrid cultivar

Type:

Expression profiling by array

Platform:

GPL11398

6 Samples

Download data: TXT

(Submitter supplied) Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases:  A Report From the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project. Acute Megakaryoblastic Leukemia (AMKL) accounts for ~10% of childhood acute myeloid leukemia (AML).  Although AMKL patients with down syndrome (DS-AMKL) have an excellent 5 year event-free survival (EFS), non-DS-AMKL patients have an extremely poor outcome with a 3 year EFS of less than 40%. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

14 Samples

Download data: CEL

(Submitter supplied) Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases:  A Report From the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project. Acute Megakaryoblastic Leukemia (AMKL) accounts for ~10% of childhood acute myeloid leukemia (AML).  Although AMKL patients with down syndrome (DS-AMKL) have an excellent 5 year event-free survival (EFS), non-DS-AMKL patients have an extremely poor outcome with a 3 year EFS of less than 40%. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

29 Samples

Download data: CEL

(Submitter supplied) Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high value lipid products. more...

Organism:

Nannochloropsis oceanica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15388

2 Samples

Download data: FASTA, GFF, GTF, TXT

(Submitter supplied) The NimbleGen cattle tick custom microarray based on the BmiGI.V2 database of R. microplus ESTs was used to screen the resulting mRNA harvested from ticks treated with the tick Ubiquitin-63E 600bp dsRNA in comparison to controls. A total of 144 ESTs including TC6372 (Ubiquitin-63E) were down-regulated with 136 ESTs up-regulated following treatment. The results obtained substantiated the knockdown phenotype with ESTs identified as associated with ubiquitin proteolysis as well as oogenesis, embryogenesis, fatty acid synthesis and stress responses. more...

Organism:

Rhipicephalus microplus

Type:

Expression profiling by array

Platform:

GPL10125

8 Samples

Download data: TXT

(Submitter supplied) A data set of normal epithelium, serous ovarian surface epithelial-stromal tumors (benign and type II malignancies), stroma distal to tumor, and stroma adjacent to tumor (50 samples total). Additional cel files are included which represent replicate sampling from patients, and cel files that failed quality control but may be bioinformatically interesting. Additional replicate or failed cel files were not included in the final analysis (and so these samples were not included in the matrix). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

72 Samples

Download data: CEL

(Submitter supplied) In the search for renewable sources of energy, bioethanol stands out as a benchmark biofuel because its production is based on a proven technological platform. Bioethanol is produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4414

3 Samples

Download data: GPR

(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. more...

Organism:

Homo sapiens

Type:

Expression profiling by SAGE

Platform:

GPL4

327 Samples

Download data

(Submitter supplied) The unicellular cyanobacterium Synechocystis sp. PCC 6803 is a model system for studying biochemistry, genetics and molecular biology of photobiological processes. Despite its importance in basic and applied research, the genome-wide picture of transcriptional regulation in this bacterium is limited. Characteristic transcriptional responses to changes in the growth environment are expected to provide a scaffold for describing the Synechocystis transcriptional regulatory network as well as efficient means for functional annotation of genes in the genome. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Dataset:

GDS3745

Platform:

GPL7016

27 Samples

Download data: GPR

Analysis of cyanobacterium cultures grown under sulfur starvation conditions for up to 72 hrs. During S limitation, production of hydrogen, a clean and sustainable energy carrier, increases substantially. Results provide insight into gene expression changes during the transition to S starvation.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array, log2 ratio, 3 stress, 11 time sets

Platform:

GPL7016

Series:

GSE11970

27 Samples

Download data: GPR

(Submitter supplied) The series was designed to obtain gene expression patterns of TNF-alpha stimulated CaCo-2 cells. Keywords: TNF-alpha stimulation

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL284

33 Samples

Download data

(Submitter supplied) The series was designed to obtain gene expression patterns of TNF-alpha stimulated THP-1 cells. Keywords: TNF-alpha stimulation

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL284

15 Samples

Download data