GEO DataSets

(Submitter supplied) Background: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequenced long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

10 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: BED, BEDGRAPH, FA

(Submitter supplied) We combine two experimental high-throughput sequencing methods to identify new 2'-O-methylation sites in human and assign snoRNA guides to sites with previously unknown guides.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: BED, FA

(Submitter supplied) We combine two experimental high-throughput sequencing methods to identify new 2'-O-methylation sites in human and assign snoRNA guides to sites with previously unknown guides.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Small non-coding RNAs function in concert with Argonaute (Ago) proteins to regulate gene expression at the level of transcription, mRNA stability or translation. Ago proteins bind small RNAs and form the core of silencing complexes. Here we report the analysis of small RNAs associated with human Ago1 and Ago2 revealed by immunoprecipitation and deep sequencing. Among the reads we find small RNAs originating from the small nucleolar RNA (snoRNA) ACA45. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9178

2 Samples

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(Submitter supplied) Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL20301

15 Samples

Download data

(Submitter supplied) Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a viral RNA-binding protein ORF57 that plays an essential role in posttranscriptional regulation of viral gene expression. Ectopice expression of KSHV ORF57 in HEK293T cells was evaluated on its effect on host gene expression in the study, with the cells transfected with an empty vector serving as a control.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Primari effusion lymphoma are (PEL) patient-derived transformed B-cells harboring latent Kaposi's sarcoma-associated herpesvirus (KSHV). The treatment of PEL cells with valproic acid (VA) leads to reactivation of KSHV and viral lytic replication. The aim of this project is to evaluate the effect of KSHV lytic infection on expression of the host transcriptome.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 is a viral RNA-binding protein essential for viral lytic gene expression. ORF57 binds to target RNA directly via interaction with cellular cofactors. To investigate the entire repertoire of ORF57-associated RNAs we performed UV cross-linking immunoprecipitatin (CLIP) experiment using an affinity-purified, highly specific anti-ORF57 antibody in KSHV-infected primariy effusion lymphoma BCBL-1 cells undegoing lytic virus replication.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

3 Samples

Download data: TXT

(Submitter supplied) The paired-end next-generation sequencing of all small RNAs of less than 200 nucleotides in length from four different human cell lines (SKOV3ip1, MCF-7, BJ-Tielf, INOF) allowed us to determine the exact sequence(s) and variations of human box C/D snoRNAs (small nucleolar RNAs), revealing processing patterns of this class of molecules. Two distinct groups of box C/D snoRNAs were identified based on the position of their ends with respect to their characteristic boxes and the terminal base pairing potential. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

15 Samples

Download data: TXT

(Submitter supplied) Small nucleolar RNAs (snoRNAs) are highly abundant non-coding RNAs whose canonical function is to guide the 2’-O-ribose methylation or pseudouridylation of ribosomal RNAs. They are often encoded in longer genes referred to as their host genes, the expression of which is required for their own biogenesis. Due to their very stable structure, reverse transcription of snoRNAs using standard viral reverse transcriptases is very inefficient, and does not provide an adequate view of the abundance of these small RNAs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

8 Samples

Download data: TSV

(Submitter supplied) Leukemogenesis requires enhanced self-renewal activity, which is induced by specific oncogenes. The underlying molecular mechanisms remain incompletely understood. We measured snoRNA expression in human primary AML samples that contained determined leukemia stem cells frequency. We identified that expression of C/D box snoRNAs was closely associated with leukemia stem cell frequency.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15456

20 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

4 related Platforms

94 Samples

Download data: CEL, TXT

(Submitter supplied) Amino Enhancer of Split (AES) is essential for AML1-ETO induced self-renewal and leukemogenesis. To study the effect of AES on transcription regulation in AML1-ETO expressing Kasumi-1 cells, nascent transcripts in control (shctr) and AES knockdown (shAES) Kasumi-1 cells were labelled with uridine analogue 4-thioduridine with subsequent nascent RNA purification and next generation sequencing (Nascent RNA-seq).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) We studied AES and DDX21 binding RNAs in Kasumi-1 cells stably expressing V5-tagged AES. RNA immunoprecipitation was performed with V5 antibody (for AES), DDX21 antibody and control IgG. We found that AES as well as DDX21 RIP samples showed enrichment for small nucleolar RNAs (snoRNAs) compared to control IgG. We also showed that AES and DDX21 binding snoRNAs showed significant overlap. Our studies provide mechanisms how AES regulates snoRNAs and rRNA modification.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15456

6 Samples

Download data: TXT

(Submitter supplied) Microarray gene profilling indentified snoRNAs are downstream target of Amino Enhancer of Split (AES) and are essential for AML1-ETO9a induced leukemia. Amino Enhancer of Split (Aes) is strongly induced by leukemia oncogenes AML1-ETO, PML-RARα and PLZF-RARα. With a conditional AES knockout mouse model we showed that AES is essential for AML1-ETO9a indeced leukemia. We performed gene expression microarray using mouse primary AML1-ETO9a transformed AES wildtype and knockout and showed that snoRNAs were downregulated in AES knockout cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL

(Submitter supplied) Leukemogenesis requires enhanced self-renewal activity, which is induced by specific oncogenes. The underlying molecular mechanisms remain incompletely understood. We transduced mouse lineage negative bone marrow cells (enriched for hematopoietic stem and progenitor cells) with retrovirus expressing leukemic oncogene AML1-ETO9a, MYC and MLL-AF9 as well as empty vector (MIG). We found that all three oncogenes enhanced snoRNA formation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16173 GPL15456

78 Samples

Download data: TXT

(Submitter supplied) As important roles of small RNA pathways, AGO proteins mediate interaction of incorporated small RNAs with their targets. The resolution of AGO associated small RNAs showed a significant landscape of AGO proteins and their binding small RNAs. To characterize small RNAs that associated with BmAGO2 protein in Bombyx mori, the small RNA population associated with BmAGO2 in BmN cells was extracted from the AGO immunoprecipitated complex and the small RNAs between 17nt to 50nt separated by a polyacrylamide gel electrophoresis were subjected to library construction and deep sequencing.The high throughput sequencing yielded a total of 11691441 reads, representing 813,702 unique reads with a abundance from 5731905 to 1.

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16216

1 Sample

Download data: FA, TXT