GEO DataSets

(Submitter supplied) GeoMx Digital Spatial Profiling (Nanostring) is a commercial spatial transcriptomics method to selectively analyze regions of interest within intact tissue sections. However, it is unclear how tissue decalcification affects the results of this assay, or if decalicified samples are comparable to untreated samples. For this purpose, we assembled a set of tissues that were subjected to progressive durations of incubation with ethylene-diamine-tetra-acetic (EDTA), and analyzed comparable regions of the tissue using GeoMx DSP. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

96 Samples

Download data: DCC, PKC, TXT

(Submitter supplied) Here, we profile miRNA expression at high temporal resolution (1 hr interval) from 5h to 48h at 25°C, during C. elegans postembryonic development, which identifies several miRNAs with highly dynamic concentration changes

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

44 Samples

Download data: TXT

(Submitter supplied) Here, we profile miRNA expression at high temporal resolution (1 hr interval) during C. elegans postembryonic development, which identifies several miRNAs with highly dynamic concentration changes

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

48 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

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

4 related Platforms

226 Samples

Download data

(Submitter supplied) Background and Purpose The neurological course after stroke is highly variable and is determined by demographic, clinical, and genetic factors. However, other heritable factors such as epigenetic DNA methylation could play a role in neurological changes after stroke. Methods We performed a three-stage epigenome-wide association study (EWAS) to evaluate DNA methylation associated with the difference between the National Institutes of Health Stroke Scale (NIHSS) at baseline and at discharge (ΔNIHSS) in ischemic stroke patients. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL13534 GPL29753

121 Samples

Download data: IDAT, TXT

(Submitter supplied) This study includes RNA-seq profiles of neutrophils from healthy donors and patients with inflammatory arthritis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

94 Samples

Download data: TXT

(Submitter supplied) The aim of study is to evaluate whether salidroside (S), tyrosol (T) and hydroxytyrosol (H) which are dietary phenylethanoids of natural origins have an influence on reversing gut dysbiosis induced by metabolic syndrome (MetS) mice. C57 BL/6J female mice induced by high fructose diet were established. All mice were adapted to the environment for 7 days with normal diet and sterile drinking water (DW), and randomly divided into 6 groups. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

30 Samples

Download data: TXT

(Submitter supplied) Transcriptiome dynamics of P. aeruginosa PA14 during batch growth in complex LB medium over the course of 10 h.

Organism:

Pseudomonas aeruginosa PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28328

46 Samples

Download data: TXT

(Submitter supplied) As compared to Eukaryotes, Bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs, which are thought to act in concert for the maintenance of gene translation. Here we show that in some bacteria the tRNA gene set may be partitioned in a housekeeping sub-set that sustains translation, and an inducible one that is generally silent but can be largely induced to provide functionality under particular conditions. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29232

12 Samples

Download data: TSV

(Submitter supplied) We used RNA-seq to profile gene expression changes during flg22 activated pattern-triggered immunity in multiple Brassicaceae including Capsella rubella, Cardamine hirsuta and Eutrema salsugineum as well as in multiple Arabidopsis thaliana accessions. This allows comparative transcriptomics within and across species to investigate the evolution of stress-responsive transcrption changes in these species.

Organism:

Arabidopsis thaliana; Capsella rubella; Cardamine hirsuta; Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

5 related Platforms

102 Samples

Download data: TXT

(Submitter supplied) Purpose: RNA analysis of post-mortem tissues, or thanathotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic case investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual. Methods: For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

54 Samples

Download data: TXT

(Submitter supplied) Exploration of new markers that define impaired metabolic flexibility using an acute postprandial challenge test. Healthy subjects underwent a 4-week high-fat high-calorie diet. High-fat challenges were performed in these subjects before and after the diet and in subjects with the metabolic syndrome.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

81 Samples

Download data: TXT

(Submitter supplied) Environmental factors, including substance abuse and stress, cause long-lasting changes in the regulation of gene expression in the brain via epigenetic mechanisms, such as DNA methylation. We examined genome-wide DNA methylation patterns in the prefrontal cortex (PFC, BA10) of 25 pairs of control and individuals with AUD, using the Infinium® MethylationEPICBeadChip. We identified 5,254 differentially methylated CpGs (pnominal<0.005). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

46 Samples

Download data: TXT

(Submitter supplied) Paroxysmal Nocturnal Hemoglobinuria (PNH) is a clonal disease of blood cells caused by the lack of glycosyl phosphatidyl inositol anchored proteins bound to the cell membrane. In consequence, erythrocytes lead to intravascular hemolysis upon complement activation, which promotes high risk of thrombosis, intravascular hemolytic anemia, and bone marrow failure in patients. The mechanisms of thrombosis in PNH are still poorly understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL25788

12 Samples

Download data: TXT

(Submitter supplied) We evaluated how HrrA binding in response to 4 µM heme as initial stimulus. Analysis was performed prior to the addition of heme (T0) and 0.5, 2, 4, 9, and 24 h after the heme pulse (in medium containing no other iron source).

Organism:

Corynebacterium glutamicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25746

6 Samples

Download data: BED

(Submitter supplied) Using transcriptomic we looked for changes in large-scale gene expression profiling of leukocytes of hypertensive patients with left ventricular remodeling compared to hypertensive patients without left ventricular remodeling and to control and whether these changes reflect metabolic pathway regulation already shown by positron emission tomography. Genes encoding for glycolytic enzymes were found over-expressed in the group of hypertensive patients with left ventricular remodeling. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

36 Samples

Download data: TXT

(Submitter supplied) The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. Unfortunately, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI) to address these problems. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17143

102 Samples

Download data: XLSX

(Submitter supplied) Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. Systematic identification and function analysis of miRNA under chilling stress could be helpful to clarify the molecular mechanism of chilling resistance. In the present study, two independent small RNA libraries from leaves of vegetable soybean were constructed, and sequenced with the high-throughput Illumina Solexa system. more...

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19246

3 Samples

Download data: XLS

(Submitter supplied) The nucleus accumbens plays a central role in ther regulation of reward, emotion, motivation and goal-directed behavior. Gene expression impairments in this brain region are of crucial interest to understand the neurobiological underpinnings of heroin use disorder. We used the Affymetrix HG-U133A microarray to assess gene expression in the post-mortem nucleus accumbens of human heroin users and control subjects and identified differentially expressed genes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

49 Samples

Download data: CEL

(Submitter supplied) Xylose induced effects on metabolism and gene expression during anaerobic growth of an engineered Saccharomyces cerevisiae on mixed glucose-xylose medium were quantified. Gene expression of S. cerevisiae harbouring an XR-XDH pathway for xylose utilisation was analysed from early cultivation when mainly glucose was metabolised, to times when xylose was co-consumed in the presence of low glucose concentrations, and finally, to glucose depletion and solely xylose being consumed. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL17988

30 Samples

Download data: XYS