GEO DataSets

(Submitter supplied) Systemic lupus erythematosus (SLE) is a serious autoimmune disease whose molecular pathogenesis is not well understood, especially the functions long noncoding RNAs (lncRNAs) in SLE development. In this study, we integrated the transcriptome profiles (RNA-seq) of peripheral blood mononuclear cells (PMBCs) from SLE patients and two published RNA-seq datasets to explore the expression profile of lncRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

8 Samples

Download data: TXT

(Submitter supplied) Transcriptome of human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose (HG) or high glucose with 4 uM TTR (HG+TTR) were conducted. Differentially expressed lncRNAs, mRNAs and TTR related lncRNAs and mRNA were acquired for further analysis. Functional annotation and enrichment including KEGG pathway, GO and GSEA were applied to analyze TTR regulated pathway and process. WGCNA analysis was implemented to obtain hub modules and genes. LncRNA-mRNA regulatory network were constructed based on cis, trans and ceRNA acting mode.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

9 Samples

Download data: TXT

(Submitter supplied) The multi-system involvement and high heterogeneity lead to great challenge in the diagnosis and treatment of systemic lupus erythematosus (SLE). Long non-coding RNA is a type of RNA greater than 200 nucleotides that does not encode proteins. LncRNA is a key regulator of gene expression in the immune system and is involved in the pathogenesis of a variety of autoimmune diseases, including SLE. In this work, we performed transcriptome sequencing and microarray analysis of peripheral blood mononuclear cells (PBMC) from freshly isolated healthy controls (n=5) and SLE patients (n=5) to analyze the expression of novel lncRNAs and mRNAsand explore their potential as biomarkers and their correlation with clinical features.

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

10 Samples

Download data: TXT

(Submitter supplied) We report transcriptional profiles of placentas from systemic lupus erythematosus pregnancies and normal full-term pregnancies. We recruited 8 pregnant patients with SLE, and 8 age-matched healthy pregnant women as normal controls. RNA-seq strand-specific libraries were constructed using the VAHTS Total RNA-seq (H/M/R)Library Prep Kit. Differentially expressed genes were identified using Cuffdiff. The P-value significance threshold in multiple tests was set by the false discovery rate (FDR). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: TXT

(Submitter supplied) Recent studies have shown that alterations in the function of dendritic cells (DCs) are involved in the pathogenesis of systemic lupus erythematosus (SLE). However, the role of DCs participating in SLE remains unclear. We profiled the lncRNAs of LPS-stimulated moDCs in SLE patients compared with healthy controls.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21242

10 Samples

Download data: TXT

(Submitter supplied) long non-coding RNAs (lncRNAs) are novel non-coding RNAs which play an important part in regulating gene transcription and translation, modulating protein function, and acting as competing endogeneous RNA. Moveover, there is increasing evidence showing that aberrant expressions of lncRNAs are implicated in various cancers. Yet, their roles in systemic lupus erythematosus (SLE), a prototypical autoimmune disease, remain unknown. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL16956

9 Samples

Download data: TXT

(Submitter supplied) Dysregulation of long non-coding RNAs (lncRNAs) has been proven to be involved in the pathogenesis of coronary artery disease (CAD). However, it remains to be extensively explored.Using microarray, we performed the transcriptome-wide lncRNA and mRNAs expression profile in peripheral blood mononuclear cells (PBMCs) of 93 CAD patients and 48 healthy controls. Gene Ontology (GO) and pathway analysis for differentially expressed mRNAs was used to investigate underlying biological associations of differentially expressed lncRNAs and create path-net to depict interactions of significant pathways. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL20115

141 Samples

Download data: JPG, TXT

(Submitter supplied) To investigate the lncRNAs expression profiling in CD4+ T cells of systemic lupus erythematosus (SLE) patients, we have employed “Agilent Human lncRNA 4*180K microarray” as a discovery platform to identify lncRNAs and mRNAs expression signatures in CD4+ T cells between SLE patients and normal controls. CD4+ T cells were isolated from peripheral blood mononuclear cells (PBMCs) of peripheral blood in SLE patients and normal controls, respectively.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL30476

12 Samples

Download data: TXT

(Submitter supplied) To explore the long non-coding RNA (lncRNA) expression pattern of congenital lung malformations on a genome-wide scale and investigate their potential biological function in four types of congenital lung malformations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

15 Samples

Download data: CSV

(Submitter supplied) Systemic lupus erythematosus patients exhibit remarkable heterogeneity in clinical manifestations and autoantibody repertoires. This complexity poses major barrier in diagnosis and effective treatment of SLE. To address this we studied the SLE patients in groups categorized on the basis of distinct sera autoantibodies. SLE patients were segregated into three group based on the presence of autoantibodies against i) dsDNA only ii) ENA (extractable nuclear antigens) only or iii) both.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: XLSX

(Submitter supplied) In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

52 Samples

Download data: TXT

(Submitter supplied) RNA-seq technology was used to detect the differentially expressed LncRNAs and mRNAs between five paired pSS patients and healthy control PBMCs. In this study, 44 out of 1772 LncRNAs and 1034 out of 15424 mRNAs were expressed differentially in the PBMCs of pSS patients.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

10 Samples

Download data: TXT

(Submitter supplied) Long non-coding RNAs (lncRNAs) are pervasively expressed and have been reported as potential biomarkers and therapeutic targets in various diseases, including systemic lupus erythematosus (SLE). However, there was limited information about lncRNAs expression in kidney tissue with lupus nephritis (LN), a serious complication of SLE. To explore the underlying molecular and cellular mechanisms of lncRNAs during pathogenesis of LN, RNA sequencing (RNA_seq) was performed to determine the lncRNAs and mRNAs expression of kidney tissues from LN (MRL/lpr) and control mouse. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: TXT

(Submitter supplied) To investigate the aberrant expressed lncRNA and mRNA and identify the potential lncRNA correlated with core mRNA in LSCC, we screened lnRNA and mRNA expression profile in 9 pairs of primary Stage IV LSCC tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays, conducted in-depth integrated bioinformatics analysis of lncRNA and mRNA, and performed qRT-PCR assays to further validate their expressions in an independent cohort of 30 pairs tissue samples

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platform:

GPL17843

18 Samples

Download data: TXT

(Submitter supplied) Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing.

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

6 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL10558

110 Samples

Download data

(Submitter supplied) Our study has demonstrated that significant number of differential genes in SLE was involved in IFN, TLR signaling pathways and inflammatory cytokines. The enrichment of differential genes has been associated with aberrant DNA methylation, which may be relevant to the pathogenesis of SLE. Our observations laid the groundwork for further diagnostic and mechanistic studies of SLE and LN.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

55 Samples

Download data: TXT

(Submitter supplied) SLE patients are always with various disease manifestation. Various cytokines are pointed interacting and playing pathological roles in SLE although the etiopathology is still obscure. In this study, we aimed to investigate the effects of cytokine interactions in the immune response of SLE patients. Overexpressed interferon-inducible(IFI) genes were confirmed in peripheral blood from SLE patients. Using network-based analysis on the immune response-related genes, several networks including cytokines such as TNF and IFN-γ, or beta-estradiol(E2), were constructed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1291

17 Samples

Download data: TXT

(Submitter supplied) The transcription factor Bach2 is a critical negative regulator of Tfh cell differentiation, especially IL-4 subset. Tfh cells from the mesenteric lymph nodes of WT and Bach2 CD4 conditional KO mice were collected to process the Rna-seq. Mechanistically, Bach2 may limit abnormal IL-4-produicng Tfh cell formation by repressing c-Maf, CXCR5 and IL-4.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: CSV

(Submitter supplied) Systemic lupus erythermatosus (SLE) is a complex autoimmune disease, and epigenetic study is promissing for illustrating the mechanisms of SLE pathogenesis. Assay for transposase accessible chromatin in single cells sequencing (scATAC-seq) shows priority to trackle this barrier. Thus, scATAC-seq was applied to difine the landscape of active regulatory DNA in systemic lupus erythermatosus (SLE) at single cell resolusion. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23227

2 Samples

Download data: BED, MTX, TSV