GEO DataSets

(Submitter supplied) Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18214

59 Samples

Download data: CSV, GTF

(Submitter supplied) Poriferans, like the demosponge Amphimedon queenslandica, are the earliest diverging metazoans and may hold the key to understanding the evolution of metazoan pathways. A. queenslandica exhibits a biphasic lifecycle, with free-swimming larvae and sessile adult stages. To study changes in the transcriptome during this period of morphological and ecological transition, we generated poly(A) fragment libraries for A. more...

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13724

11 Samples

Download data: WIG

(Submitter supplied) Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, the landscape of lncRNAs is largely unclear in Sus scrofa. Here we performed stranded RNA-seq on total RNA libraries from over 100 samples of Sus scrofa tissues. We identified 10,813 lncRNAs in Sus scrofa, of which 9,075 are novel. 57% of these lncRNAs were conserved in both human and mouse. These conserved lncRNAs tend to be more tissue-specific than pig-specific lncRNAs, and enriched in reproducible organs (i.e. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10945 GPL11429

13 Samples

Download data: FA, TXT

(Submitter supplied) We collected the ovary samples at 49 days post coitus in Large White and Meishan adult female pigs, identified the differentially expressed protein coding genes and long non-coding RNAs between these two breeds. three individuals of each breed were harvested as biological replicates.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19176

6 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

34 Samples

Download data: TXT

(Submitter supplied) Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects (CHDs). Transcriptome programming during perinatal stages is important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

17 Samples

Download data: TXT

(Submitter supplied) Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects (CHDs). Transcriptome programming during perinatal stages is important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

17 Samples

Download data: TXT

(Submitter supplied) We sequenced 2 heart samples from human fetal donors and detected the differential expressed mRNAs and lncRNAs. The network of significant differential expressed transcripts could be associated to developmental program.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B-cell differentiation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112 GPL10999

61 Samples

Download data: BED, TXT, WIG

(Submitter supplied) BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacetylation through HDAC3, antagonized p300 activity and repressed transcription, but without decommissioning enhancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15433 GPL10999 GPL11154

46 Samples

Download data: BED, BW, TXT, WIG

(Submitter supplied) This study details the content and dynamics of the long non-coding transcriptome during D. discoideum development, providing an important compendium to the well-characterized protein coding transcriptome. Applying a novel sample preparation method, we isolated antisense and long intergenic non-coding RNAs in addition to mRNAs. We describe the behavior of these different classes of RNAs that have been shown to play important regulatory roles in numerous model systems. more...

Organism:

Dictyostelium discoideum

Type:

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

Platform:

GPL22784

23 Samples

Download data: TXT, XLSX

(Submitter supplied) Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

38 Samples

Download data: BED, XLS

(Submitter supplied) To explore the circadian regulations of Bmal1, we examined the transcriptome changes in mouse livers upon Bmal1 knock out at two circadian time points, CT0 and CT12. To explore the circadian regulations of Nr1d1, we examined the transcriptome changes in mouse livers upon Nr1d1 knock out at two circadian time points, CT0 and CT12. To explore interactome of lnc-Crot, 4C-seq was performed with lnc-Crot as bait region at CT6 and CT18.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

26 Samples

Download data: TXT

(Submitter supplied) Circadian rhythms are daily physiological and behavioral changes governed by an internal molecular clock, and dysfunctions in circadian rhythms have long been associated with various neurodegenerative diseases. Abnormal sleep-wake cycle often precedes the onset of cognitive and motor symptoms in patients, while the pathological changes may further exacerbate the disturbance in circadian cycle. It is unclear whether dysregulated circadian rhythm is a consequence of, or a contributing factor for, neurodegeneration. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

35 Samples

Download data: TXT

(Submitter supplied) To explore the circadian regulations of Bmal1, we examined the transcriptome changes in mouse livers upon Bmal1 knock out at two circadian time points, CT0 and CT12.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. more...

Organism:

Mus musculus castaneus; Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

9 Samples

Download data: TXT, WIG

(Submitter supplied) To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

8 Samples

Download data: TXT

(Submitter supplied) To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

8 Samples

Download data: TXT

(Submitter supplied) To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using stranded single-end RNA-seq based on poly(A) selection.

Organism:

Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18523

2 Samples

Download data: TXT

(Submitter supplied) To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using non-directional paired-end RNA-seq based on poly(A) selection.

Organism:

Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17914

2 Samples

Download data: TXT