Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell dissection of long non-coding RNAs pivotal for embryonic hematopoietic stem cell development

ABSTRACT: Single-cell dissection of long non-coding RNAs pivotal for embryonic hematopoietic stem cell development

PROVIDER: PRJNA428181 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6433630_1.fastq.gz	Fastqsanger.gz
	SRR6433630_2.fastq.gz	Fastqsanger.gz
	SRR6433640_1.fastq.gz	Fastqsanger.gz
	SRR6433640_2.fastq.gz	Fastqsanger.gz
	SRR6433650_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 134

Similar Datasets

Single-cell dissection of long non-coding RNAs pivotal for embryonic hematopoietic stem cell development

Project description:In mammalian embryos, the stepwise generation of hematopoietic stem cells (HSCs) from endothelial precursors and pre-hematopoietic stem cells (pre-HSCs) is stringently modulated by signaling pathways and transcription factors. Nevertheless, the understanding of regulatory strength and mechanism by non-coding RNA (ncRNA) remains entirely lacking. Taking advantage of our capacity to capture rare single pre-HSCs and HSCs in vivo and accordingly generate the single-cell transcriptome datasets, here we presented the first long non-coding RNA (lncRNA) landscape of HSC development at single-cell resolution. Combining bioinformatics analysis and functional screening, we identified 6 lncRNAs showing influence on hematopoietic progenitor generation in vitro. Moreover, endothelial disruption of H19 in vivo resulted in defective emergence of functional pre-HSCs and HSCs in aorta-gonad-mesonephros region, albeit with unperturbed development of erythro-myeloid progenitors in yolk sac. Single-cell RNA sequencing revealed that H19 deficient pre-HSCs (The DMR region of H19 was knocked out in the "KO" samples) possessed similar molecular pattern with endothelial cells, suggesting their severe blockade during hematopoietic transition. Methylation sequencing of pre-HSCs further demonstrated hyper methylation on promoter region of several master hematopoietic transcription factors, including Runx1 and Spi1, by H19 deficiency. Taken together, our study identified H19 as the first non-coding gene indispensable for endothelial-to-HSC transition, and the single-cell lncRNAomics map should be valuable for exploring epigenetic control of HSC generation and regeneration.

2020-12-01 | GSE108653 | GEO

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

Long non-coding RNAs control hematopoietic stem cell function.

Project description:Hematopoietic stem cells (HSCs) possess unique gene expression programs that enforce their identity and regulate lineage commitment. Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and cell fate decisions, although their functions in HSCs are unclear. Here we profiled the transcriptome of purified HSCs by deep sequencing and identified 323 unannotated lncRNAs. Comparing their expression in differentiated lineages revealed 159 lncRNAs enriched in HSCs, some of which are likely HSC specific (LncHSCs). These lncRNA genes share epigenetic features with protein-coding genes, including regulated expression via DNA methylation, and knocking down two LncHSCs revealed distinct effects on HSC self-renewal and lineage commitment. We mapped the genomic binding sites of one of these candidates and found enrichment for key hematopoietic transcription factor binding sites, especially E2A. Together, these results demonstrate that lncRNAs play important roles in regulating HSCs, providing an additional layer to the genetic circuitry controlling HSC function.

| S-EPMC4388783 | biostudies-literature

Single-cell dissection of human hematopoietic reconstitution after allogeneic hematopoietic stem cell transplantation

Project description:Single-cell dissection of human hematopoietic reconstitution after allogeneic hematopoietic stem cell transplantation

| PRJNA932251 | ENA

Massively parallel functional dissection of schizophrenia associated non-coding genetic variants

Project description:Massively parallel functional dissection of schizophrenia associated non-coding genetic variants

| PRJNA937652 | ENA

Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (RNA-Seq)

Project description:Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. Whether and how lncRNAs might control hematopoietic stem cell (HSC) function remains largely unknown. Here, we profiled the transcriptome of purified long-term HSCs by deep RNA-sequencing and identified thousands of un-annotated transcripts of which 323 are predicted to be lncRNAs. Comparison of their expression in differentiated lineages represented by B cells (B220+) and Granulocytes (Gr1+), revealed that 159 are likely to be HSC-specific. Knockdown of two such non-coding genes (LncHSC-2 and LncHSC-1) indicated that they regulate HSC lineage differentiation, possibly via targeting cell cycle regulators and chromatin modification enzymes. Taken together, we comprehensively identify lncRNAs in HSC and show to examples that play important roles in HSC function.

2014-12-30 | GSE53928 | GEO

Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIP-Seq)

Project description:Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. Whether and how lncRNAs might control hematopoietic stem cell (HSC) function remains largely unknown. Here, we profiled the transcriptome of purified long-term HSCs by deep RNA-sequencing and identified thousands of un-annotated transcripts of which 323 are predicted to be lncRNAs. Comparison of their expression in differentiated lineages represented by B cells (B220+) and Granulocytes (Gr1+), revealed that 159 are likely to be HSC-specific. Knockdown of two such non-coding genes (LincHSC-1 and LincHSC-2) indicated that they regulate HSC lineage differentiation, possibly via targeting cell cycle regulators and chromatin modification enzymes. Taken together, we comprehensively identify lncRNAs in HSC and show to examples that play important roles in HSC function.

2014-12-30 | GSE63276 | GEO

Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIRP-seq)

Project description:Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. Whether and how lncRNAs might control hematopoietic stem cell (HSC) function remains largely unknown. Here, we profiled the transcriptome of purified long-term HSCs by deep RNA-sequencing and identified thousands of un-annotated transcripts of which 323 are predicted to be lncRNAs. Comparison of their expression in differentiated lineages represented by B cells (B220+) and Granulocytes (Gr1+), revealed that 159 are likely to be HSC-specific. Knockdown of two such non-coding genes (LincHSC-1 and LincHSC-2) indicated that they regulate HSC lineage differentiation, possibly via targeting cell cycle regulators and chromatin modification enzymes. Taken together, we comprehensively identify lncRNAs in HSC and show to examples that play important roles in HSC function.

2015-03-13 | GSE66819 | GEO

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

Massively parallel functional dissection of schizophrenia associated non-coding genetic variants [MPRA]

Project description:Massively parallel functional dissection of schizophrenia associated non-coding genetic variants [MPRA]

| PRJNA937666 | ENA