GEO DataSets

(Submitter supplied) In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL4914

3 Samples

Download data: BAR, CEL

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL24676 GPL24247

42 Samples

Download data: BW

(Submitter supplied) To understand the effect of U1 AMO treatment on wdr33 binding profile , we carried out CstF64 iCLIP-seq experiments in HeLa cells treated with either control or U1 AMO.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

4 Samples

Download data: BW

(Submitter supplied) To understand the effect of U1 AMO treatment on chromatin binding profiles of core 3' processing factors, we carried out ChIP-seq analysis for several core 3' processing factors after control and U1 AMO treatment

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

46 Samples

Download data: BW

(Submitter supplied) Control and U1 AMO were transfected into Hela cells, Ribosome-associated RNAs were purified and sequenced in Novaseq platform.To compare the translation efficiency, mRNA-seq were performed in parallel.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

8 Samples

Download data: TDF

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

78 Samples

Download data: BW, TDF

(Submitter supplied) To understand if U1-AMO induced truncated forms of mRNAs could be exported into cytoplasm, we performed 3'-seq analysis in the cytoplasmic RNAs of control and U1 AMO treated Hela cells

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

4 Samples

Download data: BW

(Submitter supplied) To understand the effect of U1 AMO treatment on CstF64 binding profile , we carried out CstF64 iCLIP-seq experiments in HeLa cells treated with either control or U1 AMO.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

4 Samples

Download data: TDF

(Submitter supplied) To understand the effect of FUS protein knock-down on poly(A+) RNAs profiles, we carried out control and FUS depletion (using synthetic siRNAs) experiments followed by poly(A+) RNA 3'-seq anlyais using lexogen kit (016.024)in HeLa cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: BW

(Submitter supplied) To understand the effect of U1 snRNP-specific proteins on poly(A+) RNAs profiles, we carried out control and U1A, U1C, U1-70k depletion (using synthetic siRNAs) experiments followed by poly(A+) RNA 3'-seq anlyais using lexogen kit (016.024)in HeLa cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BW

(Submitter supplied) RNA-Seq analysis of SSA treated cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

2 Samples

Download data: BW

(Submitter supplied) Full-length transcription in the majority of human genes depends on U1 snRNP (U1) to co-transcriptionally suppress transcription-terminating premature 3’-end cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals (PASs) in introns. However, the mechanism of this U1 activity, termed telescripting, is unknown. Here, we captured a complex, comprising U1 and CPA factors (U1–CPAFs), that binds intronic PASs and suppresses PCPA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

22 Samples

Download data: BW

(Submitter supplied) In an attempt to discover potential RNA-RNA interactions in mRNA 3’ processing regulation, we developed PAS-CLASH (PolyA Site-Crosslinking, Ligation and Sequencing of the Hybrid) method, which combines reported CLASH and poly(A) site sequencing protocols. Briefly, HeLa cells were treated with AMT, or without AMT as control, and irradiated at 365 nm for crosslinking. Following nuclear RNA fragmentation and purification, the potential proximate RNAs/PASs were ligated on the oligo d(T)25 beads, hybrids were reverse crosslinked and amplified with the QuantSeq Rev 3' mRNA sequencing library prep kit (Lexogen, Cat. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

4 Samples

Download data: CSV

(Submitter supplied) To globally assess the effect of polyadenylation site (PAS) usage upon functional knockdown of U1 snRNP, we carried out PAS-seq analysis with control and U1 AMO-treated HeLa cells using the QuantSeq Rev 3' mRNA sequencing library prep kit (Cat. 016-24).

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

4 Samples

Download data: CSV

(Submitter supplied) To investigate whether U1C plays a role in splicing regulation in human system, we performed siRNA-mediated knockdown of U1C in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing (RNAseq)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: BIGWIG

(Submitter supplied) This project looks into how U1 levels affect cancer cell phenotype in vitro.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL11154

6 Samples

Download data: BW

(Submitter supplied) Splicing is initiated by a productive interaction of pre-mRNA and the U1 snRNP, which dictates the formation a short RNA duplex between the 5’ splice site of a pre-mRNA and the 5’ end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5’-end of the U1 snRNA shows strict conservation, despite the absence of an apparent role in duplex formation. To explore this conundrum, we varied this AU dinucleotide into to all possible permutations and analyzed the resulting molecular, biochemical, and physiological consequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8154

2 Samples

Download data: GPR

(Submitter supplied) Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

48 Samples

Download data: BIGWIG, BW, TXT

(Submitter supplied) To better understand the mechanism of U1A functions in human cells, we performed U1A iCLIP-seq analysis in HeLa cells. iCLIP-seq is a previously well-established protocol that is believed to detect protein-RNA interaction at individual-nucleotide resolution. Indeed, successful completion of U1A iCLIP-seq has helped us to illuminate more detailed mechanism through which U1 snRNP prevents mRNA PCPA (premature cleavage and polyadenylation)

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

2 Samples

Download data: BW

(Submitter supplied) Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

6 Samples

Download data: TXT