GEO DataSets

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL11154

15 Samples

Download data: BIGWIG

(Submitter supplied) RNA-sequencing has been used to obtain and observe transcriptome-wide differences that occur in two parasspeckle-deficient, MYCN-amplified/model high-risk and one paraspeckle-abundant, non-MYCN-amplified/low-risk cell lines, to decipher the role of paraspeckles in this cancer type.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BIGWIG

(Submitter supplied) RNA-sequencing has been used to obtain transcriptome-wide differences that occur in paraspeckle-deficient, MYCN-amplified/model high-risk neuroblastoma cell lines with an increase in the long non-coding paraspeckle-associated NEAT1_2 RNA, to decipher the role of paraspeckles in this cancer type.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: CSV

(Submitter supplied) To identify the RNA targets of the RNA binding proteins NONO and SFPQ in two different cell types, PARCLIP was carried out (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using a monoclonal antibody that recognises a NONO/SFPQ heterodimer. In this analysis, only the target gene NEAT1 was analysed, to show the binding sites for NONO and SFPQ in this transcript in the two cell lines.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

4 Samples

Download data: BED

(Submitter supplied) The goal of this study was to determine if the lncRNA Neat1, in addition to its structural role, may also be directly involved in the binding by base pairing of RNAs and consequently in their retention in paraspeckles

Organism:

Rattus norvegicus

Type:

Other

Platform:

GPL18694

6 Samples

Download data: CSV

(Submitter supplied) The long non-coding RNA NEAT1 (nuclear enriched abundant transcript 1) nucleates the formation of paraspeckles, which constitute a type of nuclear body that has multiple roles in gene expression. How the NEAT1 gene itself is regulated and how paraspeckles communicate with other cell compartments remains poorly understood. Here we identify regulators of NEAT1 transcription using an endogenous NEAT1 promoter-driven EGFP reporter in human cells coupled with genome-wide RNAi screens. In addition to transcription factors and chromatin modulators, the screens unexpectedly yielded gene candidates involved in mitochondrial functions as essential regulators of NEAT1 expression and paraspeckle formation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20795 GPL11154

5 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10656 GPL14550

806 Samples

Download data: TXT

(Submitter supplied) Background: Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different molecular levels in order to identify integrated subtypes. Methods: Tumor tissue from 425 primary breast cancer patients of the Oslo2 study was cut and blended before being divided into fractions for DNA-, RNA- and protein isolation, and metabolomics, allowing for representative and comparable molecular data. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

381 Samples

Download data: TXT

(Submitter supplied) To explore the effect of NEAT1 on gene transactivation induced by p53, we evaluated the changes in gene expression by RNA-seq in NEAT1 knockdown or control U2OS cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) To identify human genes whose expression is controled by nuclear paraspeckle, the microarray was carried out using the RNA samples prepared from the control and NEAT1 lncRNA knockdown HeLa cells where the nucelar paraspckels were disintegrated. NEAT1 lncRNA was eliminated by administration of antisense oligogapmer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

6 Samples

Download data: TXT

(Submitter supplied) Although thousands of long non-coding RNAs (lncRNAs) are localized in the nucleus, only a few dozen have been functionally characterized. We found that nuclear paraspeckle assembly transcript 1 (NEAT1), an essential lncRNA for the formation of nuclear body paraspeckles, is induced by poly I:C stimulation, resulting in excess formation of paraspeckles. Using microarray analysis, we investigated whether NEAT1 induction followed by excess formation of paraspeckles was involved in poly I:C-inducible gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining public microarray and RNA sequencing datasets, we identified neuroblastoma highly expressed 1 (NHEG1) as a novel 1360-bp lncRNA associated with poor outcome of NB. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

6 Samples

Download data: CEL

(Submitter supplied) We performed the scRNA-seq analysis of 6 osteosarcoma tissues based on the 10X Genomics.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(Submitter supplied) We report 6p22 locus lncRNAs, which were identified as differentially expressed between high and non-high risk neuroblastoma tumors using RNA sequencing. we identified CASC15-003 and CASC15-004 lncRNAs act as prognostic biomarker in neuroblastoma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

22 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to determine the effect of the deletion of the lncRNA Neat1 on the rhythmic gene expression in the GH4C1 cell line

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

42 Samples

Download data: CSV

(Submitter supplied) Profile of the genomic binding sites for endogenous NEAT1 in human primary keratinocytes (HEKn) maintanied for six days in high calcium-containing medium. Chromatin was isolated from gluteraldeyde-fixed nuclei of differentiated HEKn and NEAT1-associated D

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33415

20 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL33415

31 Samples

Download data: BROADPEAK, BW, TSV, TXT

(Submitter supplied) The transcription factor ΔNp63, a master regulator of epithelial biology, is involved in regulating epithelial stem cell function and maintaining the integrity of stratified epithelial tissues such as the epidermis. To this end, ΔNp63 acts as transcriptional repressor or activator towards a distinct subset of protein-coding genes and microRNAs. However, how and whether ∆Np63 regulates long non-coding RNA (lncRNAs) expression is not known. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TSV

(Submitter supplied) The transcription factor ΔNp63, a master regulator of epithelial biology, is involved in regulating epithelial stem cell function and maintaining the integrity of stratified epithelial tissues such as the epidermis. To this end, ΔNp63 acts as transcriptional repressor or activator towards a distinct subset of protein-coding genes and microRNAs. However, how and whether ∆Np63 regulates long non-coding RNA (lncRNAs) expression is not known. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: BROADPEAK, BW

(Submitter supplied) Alternative RNA 3’-end processing provides an important source of transcriptome diversification, which impacts various biological processes and the etiology of diseases, including cancer. A prime example of this is the transcript isoform switch that leads to the read-through expression of the long non-coding RNA NEAT1_2, at the expense of the shorter polyadenylated transcript NEAT1_1. Expression of NEAT1_2 is required for the formation of paraspeckles (PS), nuclear bodies that protect cancer cells from oncogene-induced replication stress and chemotherapy. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21290

6 Samples

Download data: BED, BW