Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)

ABSTRACT: Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)

PROVIDER: PRJNA751597 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15327108_1.fastq.gz	Fastqsanger.gz
	SRR15327108_2.fastq.gz	Fastqsanger.gz
	SRR15327109_1.fastq.gz	Fastqsanger.gz
	SRR15327109_2.fastq.gz	Fastqsanger.gz
	SRR15327110_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 160

Similar Datasets

Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (Illumina short-read sequencing)

Project description:Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (Illumina short-read sequencing)

| PRJNA748710 | ENA

Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)

Project description:Albeit majority of eukaryotic genome can be pervasively transcribed to a diverse population of lncRNAs and various subtypes of lncRNA have been discovered. However, the genome-wide study of miRNA-derived lncRNAs is still lacking. Here, we report that over 800 miRNA gene-originated lncRNAs (molncRNAs) generated from miRNA loci. One of them, molnc-301b from miR-301b and miR-130b, functions as an "RNA decoy" to facilitate dissociation of the chromatin remodeling protein SMARCA5 from chromatin and thereby sequester transcription and mRNA translation. Specifically, molnc-301b attenuates erythropoiesis via mitigating the transcription of erythropoietic and translation-associated genes, such as GATA1 and FOS. In addition, we have established a useful and powerful CRISPR screen platform to characterize the biological functions of molncRNAs at large-scale and single-cell level, and identified 26 functional molncRNAs in hematopoietic cells. Collectively, we focused on miRNA-derived lncRNAs, deciphered their landscape during normal hematopoiesis, and comprehensively evaluated their potential roles.

2023-10-18 | GSE181338 | GEO

Relevance study and prognostic analysis for intestinal flora disorders affecting non-coding RNA networks in patients with advanced lung cancer

Project description:Interventions: Case series:Nil Primary outcome(s): intestinal microecological disorders;blood non-coding RNAs and immune status Study Design: Randomized parallel controlled trial

| 2681498 | ecrin-mdr-crc

Non-coding RNAs in breast cancer

Project description:Using RNA CaptureSeq we annotated non-coding RNAs transcribed from genome intervals surrounding breast cancer risk signals in a range of mammary-derived tissue and cell lines.

| EGAS00001003353 | EGA

Bacterial non-coding RNAs excised from within protein-coding transcripts

Project description:Bacterial non-coding RNAs excised from within protein-coding transcripts

| PRJEB27518 | ENA

Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (Illumina short-read sequencing)

Project description:Genome-wide transcription produces a complex population of transcripts and a wide variety of functional lncRNAs occasionally evolve from them. Here, we identify and characterize miRNA gene originated lncRNAs (molncRNAs) by employing Pacific Biosciences long-read sequencing. Combining with RNA-sequencing in differentiating hematopoietic erythrocytes, we construct a global molncRNA landscape during human erythropoiesis. Among them, miR-301b and miR-130b originated lncRNA, molnc-301b, orchestrates erythropoiesis independent of miRNAs. Mechanistically, molnc-301b attenuates the transcription of a series of erythropoietic and translation-associated genes by antagonizing SMARCA5's chromatin binding. Furthermore, molnc-301b perturbs translation of key erythroid mRNAs selectively, as GATA1 and FOS. Our findings identify a novel class of lncRNA and reveal the essential role of molnc-301b in erythroid differentiation. Of note, molnc-301b orchestrates erythropoiesis via jointly controlling the transcription and translation of key erythroid regulators. In addition, we finally establish functional molncRNA screen platform by using large-scale pooled CRISPR-based single-cell RNA-seq, and uncover 36 functional molncRNAs in erythrocytes. These results thus unearth a previously unannotated class of lncRNAs and provide a useful platform for the discovery and functional study of molncRNAs.

2023-10-18 | GSE180565 | GEO

Long non-coding RNAs in B cells

Project description:Long non-coding RNAs in B cells

| PRJNA292725 | ENA

Circulating non-coding RNAs in Huntington disease

Project description:Circulating non-coding RNAs in Huntington disease

| PRJNA705157 | ENA

Comprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts

Project description:Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-seq data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ~69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the current inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames (ORFs) from being regarded as protein-coding.

2020-01-09 | PXD014553 | Pride

Dissecting non-coding and pathogen RNA-protein interactomes

Project description:RNA-protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and non-human RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and non-human transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2 bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs. Characterization of non-coding and pathogen RNA-protein interactions using an automated computational pipeline and improved iCLIP biochemistry

2014-11-18 | E-GEOD-59840 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data