GEO series

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]

GSE77629 Homo sapiens (human) Other 24 samples Submitted 2016/03/28 Platform GPL16791

At a glance

human · 24 samples

Organism: Homo sapiens (human)
Samples: 24 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function.

Read the full summary ↓

However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.

This dataset

Open GSE77629 in finder → Find more human datasets →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE77629_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA311053 and SRA study SRP069351. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27018577) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 24 more — browse all 24 samples with per-sample file links →

Datasets on a similar topic

GSE311747 RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution [CLIP] 27 samples shares clip, enables, binding
GSE21918 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data 15 samples shares clip, transcriptome-wide, binding
GSE213806 Transcriptome-wide mapping of RNA:protein interactions of PRPF8 and SNRNP200 (BRR2) with retinitis pigmentosa (RP) mutations by iCLIP 27 samples shares clip, transcriptome-wide
GSE261913 Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-Wide 134 samples shares transcriptome-wide, binding
GSE298715 Primary human intestinal organoids recapitulate enteric infection of monkeypox virus and enable scalable drug discovery 18 samples shares discovery, scalable
GSE317890 Transcriptomic profiling of interferon responses induced by IVT sgRNAs in CRISPRi HEK293T cells 360 samples shares 293t
GSE215323 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_BPK25_ChIP_Seq] 53 samples shares 293t
GSE278192 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T ChIP-seq] 45 samples shares 293t

Search all human datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.