GEO DataSets

(Submitter supplied) Low back pain continues to be a major public health problem worldwide. In this study, we used single-cell transcriptomic analysis to identify new specific biomarkers for nucleus pulposus (NP) and annulus fibrosis (AF) cells and to define cell populations within non-degenerating and degenerating human intervertebral discs (IVD). Freshly isolated human NP and AF cells were separately isolated from non-degenerating (nD) and degenerating (D) discs of the same individual. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: H5

(Submitter supplied) We investigated the heterogeneous cell populations composing Bovine Intervertebral Discs (IVDs) through single cell RNA sequencing technologies. The assay sequenced over 14,000 cells composing 5 bovine discs from 3 unique bovine tails. Through both established and custom analysis pipelines, we characterize cell heterogeneity between populations of Nucleus Pulposus and Annulus Fibrosus cells. We further characterize populations of Endothelial, Muscle, Immune, and Notochord.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

5 Samples

Download data: MTX, RDS, TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

24 Samples

Download data: MTX, TSV

(Submitter supplied) Elucidating how cell populations promote onset and progression of intervertebral disc degeneration (IDD) has the potential to enable more precise therapeutic targeting of cells and mechanisms. Single cell RNA-sequencing (scRNA-seq) was performed on surgically separated annulus fibrosus (AF) (19,978; 26,983 cells) and nucleus pulposus (NP) (20,884; 24,489 cells) from healthy and diseased human intervertebral discs (IVD). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

18 Samples

Download data: MTX, TSV

(Submitter supplied) For this study, we applied scRNA-seq to cells from surgically separated annulus fibrosus and nucleus pulposus tissues to identify A) thecellular landscapes of healthytissues, and B) characterize in detail the composition andgene regulatory networksof immature cell populations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: MTX, TSV

(Submitter supplied) Background: Low back pain is a leading cause of disability worldwide and is frequently attributed to intervertebral disc (IVD) degeneration. Though the contributions of the adjacent cartilage endplates (CEP) to IVD degeneration are well documented, the phenotype and functions of the resident CEP cells are critically understudied. To better characterize CEP cell phenotype and possible mechanisms of CEP degeneration, bulk and single-cell RNA-Sequencing of non-degenerated and degenerated CEP cells were performed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: MTX, TSV

(Submitter supplied) Background: Low back pain is a leading cause of disability worldwide and is frequently attributed to intervertebral disc (IVD) degeneration. Though the contributions of the adjacent cartilage endplates (CEP) to IVD degeneration are well documented, the phenotype and functions of the resident CEP cells are critically understudied. To better characterize CEP cell phenotype and possible mechanisms of CEP degeneration, bulk and single-cell RNA-Sequencing of non-degenerated and degenerated CEP cells were performed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) Failure of the nucleus pulposus (NP) causes intervertebral disc (IVD) disease and associated low-back pain, which are highly prevalent among the aged populations. Molecular and cellular changes underpinning the structural failures in age-associated IVD diseases (IDDs) remain poorly elucidated. Here, we first identified that TAGLN, which encodes the cytoskeleton regulator transgelin, was transcribed in healthy NPs of both human and mouse, but diminished with ageing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

5 Samples

Download data: TSV

(Submitter supplied) Failure of intervertebral disc components, e.g. the nucleus pulposus causes intervertebral disc disease and associated low-back pain. Despite the high prevalence of disc disease, the changes in intervertebral disc cells and their regenerative potential with ageing and degeneration are not fully elucidated. Understanding the cell lineage, cell differentiation and maintenance of nucleus pulposus may have therapeutic application for the regeneration of degenerative disc, with significant impact for healthy ageing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: MTX, TSV

(Submitter supplied) The pathophysiology of intervertebral disc (IVD) degeneration is not entirely understood; however, environmental and endogenous factors under genetic predisposition are considered to initiate the degenerative changes of human IVDs. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT, TXT

(Submitter supplied) It has been shown that the divergence of NPCs plays an important role in the progression of intervertebral disc degeneration (IVDD). We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of NPCs in the IVDD.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791

13 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) N6-methyladenosine (m6A) is the most prevalent modification of eukaryotic cells st post-transcriptional level. The goals of this study are to compare the N6-methyladenosine modification of transcripts in normal and senescent nucleus pulposus cells using Me-RIP-seq

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20795

9 Samples

Download data: TXT

(Submitter supplied) Intervertebral disc degeneration is a leading cause of chronic low back pain. Cell-based strategies that seek to treat disc degeneration by regenerating the central nucleus pulposus hold significant promise, but key challenges remain. One of these is the inability of therapeutic cells to effectively mimic the performance of native nucleus pulposus cells, which are unique amongst skeletal cell types in that they arise from the embryonic notochord. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: MTX, TSV

(Submitter supplied) Intervertebral disc degeneration is the main cause of low back pain and the mechanism of which is far from fully revealed. Although multiple factors are related to the intervertebral disc degeneration, inflammation and matrix metabolism dysregulation are the two key factors that play an important role in degeneration. Here, we found that CHSY3 is highly related to the nucleus pulposus degeneration. We generated CHSY3 knockout mice using Crisper/Cas9 system, and the NP cells are studied in this experiment.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis of nucleus pulposus (NP) and annulus fibrosus (AF) tissues from intervertebral discs of 3-month-old mice with the conditional postnatal deletion of Sox9. The transcription factor Sox9 is essential for the maintenance and health of the intervertebral disc of mice. We examined the transcriptomic profiles of nucleus pulposus and annulus fibrosus cells in control and Sox9 conditional knock-out mice using microarrays.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

16 Samples

Download data: CEL, CHP

(Submitter supplied) Although it is well-recognized that apoptosis, senescence, and increased production of inflammatory cytokines and catabolic products are important factors in the degeneration of the human intervertebral disc, there is poor understanding of the underlying cause. The objective of the present study was to analyze gene expression patterns in the human annulus disc tissue.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1352

23 Samples

Download data: CEL

(Submitter supplied) Purpose: We used single-cell RNA-sequencing analysis of degenerating tissues of the rat IVD following lumbar disc puncture Methods: Two control, uninjured IVDs (L2-3, L3-4) and two degenerated, injured IVDs (L4-5, L5-6) from each animal were examined either at the two- or eight-week post-operative time points. The cells from these IVDs were extracted and transcriptionally profiled at the single-cell resolution Results: Unsupervised cluster analysis revealed the presence of four known cell types in both non-degenerative and degenerated IVDs based on previously established gene markers: IVD cells, endothelial cells, myeloid cells, and lymphoid cells. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

16 Samples

Download data: TXT

(Submitter supplied) Single cell RNA sequencing (scRNA-seq) analysis identified notochordal nucleus pulposus (NP) cells and chondrocyte-like NP cells in NP. Cells in human induced pluripotent stem cell-derived cartilage (hiPS-Cart) corresponded to chondrocyte-like NP cells but not to notochordal NP cells. hiPS-Cart cells changed their profile after implantation into intervertebral disks of nude rats, differentiating into two lineages that are metabolically distinct from each other. more...

Organism:

Homo sapiens; Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL28212

5 Samples

Download data: TXT, XLSX