GEO DataSets

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL21103

28 Samples

Download data: TXT

(Submitter supplied) Purpose: To reveal the small RNA profiles in the intima using traditional and PANDORA-seq methods. Methods: 3-week-old LDLR-/- male mice were fed a high cholesterol or low cholesterol diet for 9 weeks. Intimal RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing. Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: TXT

(Submitter supplied) Purpose: To investigate the effects of high cholesterol diet on the intimal transcriptome related to atherosclerosis. Methods: 3-week-old LDLR-/- male mice were fed a high cholesterol or low cholesterol diet for 9 weeks. Intimal RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing. Results: Mice fed a high cholesterol revealed upregulation in atherosclerosis and immune/inflammatory related genes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: XLSX

(Submitter supplied) Small non-coding RNAs (sncRNAs) are key molecules regulating gene expression. High-throughput RNA-seq greatly advanced sncRNA discovery; however, traditional cDNA library construction protocols generate biased sequencing results, in part due to RNA modifications that interfere with adapter ligation and reverse transcription processes, preventing the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (Panoramic RNA Display by Overcoming RNA modification Aborted Sequencing), employing a combination of enzymatic treatments to remove key RNA modifications that block adapter ligation and reverse transcription during cDNA library construction. PANDORA-Seq enables the discovery of thousands of modified sncRNAs previously undetected, mostly tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), which are tissue/cell-specifically detected across mouse brain, liver, spleen, sperm, mouse and human embryonic stem cells, and HeLa cells. Moreover, PANDORA-Seq reveals dynamic changes of tsRNAs and rsRNAs during reprogramming of induced pluripotent stem cells (iPSCs), pointing to future investigations on their potential regulatory functions.

Organism:

Homo sapiens; Mus musculus

Type:

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

4 related Platforms

201 Samples

Download data: TXT

(Submitter supplied) To identify the sncRNAs related to HBV-ACLF, we performed small RNA-seq in plasma exosomes collected from 3 normal subjects, 4 chronic hepatitis B (CHB) patients with flare and 6 HBV-ACLF patients in the discovery cohort.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21290

13 Samples

Download data: TXT

(Submitter supplied) Human post-mortem brain samples from Alzheimer’s disease (AD) and control individuals were processed for small RNA-sequencing followed by comparative analyses

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL24247

31 Samples

Download data: TXT

(Submitter supplied) Purpose: To investigate the effects of DCHP expoure on F1 male hepatic metabolic disorders Methods: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks, 3 week old F1 male mice were fed with HFD for 9 weeks, glucose and insulin tolerant tests were performed at 10-11 week old, liver RNA was isolated for further transcriptome analysis Results: Mice from DCHP exposure sires displayed glucose/insulin resistant phenotype, together with upregulation in inflammatoy related genes in the liver

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: XLSX

(Submitter supplied) Purpose: To reveal the small RNA profiles in the sperm using traitional and PANDORA-seq methods Methods: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks. Sperm RNA was extracted for further processing Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. Importantly, PANDORA-seq revealed that many differentially regulated sncRNAs also undetected with traditional-seq

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

19 Samples

Download data: TXT

(Submitter supplied) In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from three strains of Trichomonas vaginalisto identify and characterize novel type of small RNAs. We detected a new type of small RNA from tranfer RNA known as tRFs and tRNA-halves.

Organism:

Trichomonas vaginalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22655

3 Samples

Download data: FA, TXT

(Submitter supplied) Transfer-RNA-Derived Small RNA (tsRNA) is s a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the brain of intracerebral hemorrhage (ICH) and sham rats at days 21. Meanwhile, tsRNA levels in ICH treated with the Traditional Chinese Medicine named Buyang Huanwu Decoction (BYHWD) were detected. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

9 Samples

Download data: XLSX

(Submitter supplied) This study annotates the NGS reads in a Sertoli cell sncRNA library. In addition to known sncRNAs, we also identified numerous novel sncRNAs expressed by Sertoli cells. Our data suggest that the Sertoli cell sncRNA transcriptome predominantly consists of miRNAs, piRNA-like RNAs, tRNAs and snoRNAs. This study reports the first comprehensive annotation of the Sertoli cell sncRNA transcriptome.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9522

1 Sample

Download data: GFF

(Submitter supplied) Purpose: Screening the sperm sncRNAs that are responsible for dairy cattle fertility is of great interest, however, exploring the fertility-associated sncRNAs in sperm and linking them with the epigenetic inheritance in bovine has not been performed yet. Here in this study, we hypothesized that some sncRNAs in bovine sperm have a great potential to be linked with direct and immediate bull fertility data and could later influence the embryo and possibly impacting the daughter fertility. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26012

10 Samples

Download data: XLSX

(Submitter supplied) The purpose of the study was to investigate the roles and possible functions of the miRNAs and tsRNAs in choroidal neovascularization (CNV).The mouse model of laser-induced CNV was conducted by laser photocoagulation and the samples were collected 7 days after laser treatment. The expression profiles of miRNAs and tsRNAs were accessed by small RNA sequencing in RPE-choroid-sclera complexes of mice in CNV group and controls. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) is the main way to mine ncRNA. The purpose of this study is to screen out tRNA-derived small RNAs (tsRNAs) that are differentially expressed in proliferative and quiescent HASMCs Methods: tsRNAs profiles of proliferative and quiescent HASMCs were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed Illumina chastity filter were used for the following analysis. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) Small non-coding RNAs (sncRNAs) are generated from different genomic loci and have important roles in biological processes, such as cell proliferation and regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNAs, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small interfering RNAs), piRNAs and plant specific 24-nt short interfering RNAs (siRNAs). more...

Organism:

Populus deltoides

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20012

11 Samples

Download data: TXT

(Submitter supplied) We report a significant number of miRNAs and other non-coding small RNAs show dramatic changes in expression during aging in C. elegans. RNAs were prepared from four diffrent timepoints during adulthood of C. elegans hermaphrodites, Day 0, 5, 8 and 12 post-L4 molt, and used for making cDNA libraries for small RNAs. Each library was sequenced using recent advances in high-throughput sequencing technology, Solexa. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

6 Samples

Download data: TXT

(Submitter supplied) The discovery of RNAs (e.g. mRNAs, non-coding RNAs) in sperm has opened the possibility that sperm may function in delivering additional paternal information aside from solely providing the DNA1. Increasing evidence now suggests that sperm small non-coding RNAs (sncRNAs) can mediate intergenerational transmission of paternally acquired phenotypes, including mental stress2, 3 and metabolic disorders4-6. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL13112

16 Samples

Download data: TXT

(Submitter supplied) One unmet challenge in current lung cancer diagnosis is to accurately differentiate lung cancer patients from those with other lung diseases with similar clinical symptoms and radiological features. Previous studies have reported cases of misdiagnosis for patients with lung cancer mimicking pulmonary tuberculosis (TB) or for TB patients with multiple lung nodules mimicking lung cancer progression, which is concerning for clinical practice in TB-endemic countries/regions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

35 Samples

Download data: TXT

(Submitter supplied) One unmet challenge in current lung cancer diagnosis is to accurately differentiate lung cancer patients from those with other lung diseases with similar clinical symptoms and radiological features. Previous studies have reported cases of misdiagnosis for patients with lung cancer mimicking pulmonary tuberculosis (TB) or for TB patients with multiple lung nodules mimicking lung cancer progression, which is concerning for clinical practice in TB-endemic countries/regions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

59 Samples

Download data: TXT