GEO DataSets

(Submitter supplied) Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20795 GPL16791 GPL11154

110 Samples

Download data: BW, NARROWPEAK

(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:

GPL11154 GPL16791 GPL20795

152 Samples

Download data: BED, BW, NARROWPEAK, TXT

(Submitter supplied) Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

38 Samples

Download data: BED, BW

(Submitter supplied) Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(Submitter supplied) We profile gene expression upon circCDYL KD in HepG2 cells and in two bladder cancer cell lines J82 and UMUC3 as well as upon knockdown of the RNA binding proteins (RBP) GRWD1, IGF2BP1, and IGF2BP2 in J82 and UMUC3

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: TXT

(Submitter supplied) We profile the expression of circular RNAs (circRNAs) upon KHSRP KD in HepG2 and K562 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) Background: Cellular RNA binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are not well-characterized and remain undefined in hematopoietic cells. Results: We first provide a full view of RBPs' distribution pattern in the nucleus and screen for chromatin-enriched RBPs (Che-RBPs) in different human cells. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL20795

84 Samples

Download data: BED, TXT

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

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

378 Samples

Download data: BED, BW

(Submitter supplied) Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

228 Samples

Download data: BED, BW

(Submitter supplied) Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

150 Samples

Download data: BED, BW

(Submitter supplied) Increasing evidence suggests that diverse RNA binding proteins interact with regulatory RNAs to regulate transcription. RBFox2 is a ubiquitous RNA binding protein with prevalent expression in stem cells, heart, and brain. Here, we report a systematic dissection of the RBFox2-regulated RNA program in the mouse heart, demonstrating its essential function for organizing the contractile apparatus and excitation-contraction (EC) coupling by modulating alternative splicing and microRNA activity. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

33 Samples

Download data: BW, XLSX

(Submitter supplied) Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, studied a collection of CLIP-Seq (CrossLinked ImmunoPrecipitation) experiments mapping the RNA binding sites for a diverse set of 46 human proteins across 68 experiments to explore the role of TEs in post-transcriptional regulation genome-wide via RNA-protein interactions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: DIFF

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: WIG

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

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: BED, BW, WIG

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

3 Samples

Download data: BW, WIG

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: BED, WIG

(Submitter supplied) Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: WIG

(Submitter supplied) Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein-RNA complexes and polyA pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non polyA RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of polyA pulldown. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

6 Samples

Download data: TSV

(Submitter supplied) Latency-associated nuclear antigen (LANA), a multifunctional protein expressed by the Kaposi sarcoma-associated herpesvirus (KSHV) in latently-infected cells, is required for stable maintenance of the viral episome. This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL9115 GPL16791

33 Samples

Download data: BED, GTF, TXT

(Submitter supplied) RNA-binding proteins (RBPs) have essential functions during germline and early embryo development. However, current methods are unable to identify the in vivo targets of an RBP in those rare cells. Here, by coupling RBP-mediated reverse transcription termination with linear amplification of cDNA ends and sequencing, we present the LACE-seq method for identifying RBP-regulated RNA networks at or near the single-oocyte level. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

5 related Platforms

55 Samples

Download data: BIGWIG, BW, TXT