GEO DataSets

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20795 GPL15520

66 Samples

Download data: BED

(Submitter supplied) We utilized the stranded RNA-seq and small RNA-seq to identify and quantify RNA editing events located in miRNA and mRNA loci.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) We utilized the targeted RNA-seq to identify and quantify RNA editing events located in miRNA and mRNA loci.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

60 Samples

Download data: BED

(Submitter supplied) modENCODE_submission_2744 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. more...

Organism:

Oryza sativa

Type:

Expression profiling by MPSS

Platforms:

GPL3777 GPL3776

5 Samples

Download data

(Submitter supplied) Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15167

2 Samples

Download data: TXT

(Submitter supplied) Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. more...

Organism:

Schizosaccharomyces pombe

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL17225

4 Samples

Download data: TXT

(Submitter supplied) Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

8 Samples

Download data: TXT

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

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17225 GPL15167

18 Samples

Download data

(Submitter supplied) Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17225

4 Samples

Download data: TXT

(Submitter supplied) High-throughput sequencing of Drosophila melanogaster small RNAs. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Keywords: High-throughput solexa sequencing

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data

(Submitter supplied) RNA-seq analyses of leaves from drought stressed rice plants was performed, producing differential expression profiles of genes containing coding RNAsand noncoding RNAs.

Organism:

Oryza sativa

Type:

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

Platform:

GPL19290

4 Samples

Download data: XLSX

(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) Purpose: We carried out small RNA sequencing to determine miRNA expression patterns of hippocampus and frontal cortex in six inbred mouse strains. We analyzed miRNA expression levels, isomiR distribution and miRNA editing events. Methods: We constructed small RNA libraries starting from the total RNA extracted from the hippocampus and frontal cortex of three animals per strain. The sequencing was carried out using Illumina HiSeq2000 (single-end). more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

36 Samples

Download data: VCF

(Submitter supplied) MicroRNAs are small non-coding RNAs that are critical in post-transcriptional regulation. According to the latest miRBase (v22), there are 617 annotated pre-miRNAs in Macaca mulatta, which is much less than 1917 in human, although both of these two species are primates. To improve the annotation of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from 8 tissues and perform comprehensive analysis of these profiles. more...

Organism:

Macaca mulatta

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14954

12 Samples

Download data: TXT

(Submitter supplied) Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by genome tiling array

Platforms:

GPL8283 GPL8282

4 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11305

4 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

3 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9052 GPL11305

28 Samples

Download data: BED, TXT

(Submitter supplied) Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

21 Samples

Download data: TXT