GEO series

Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP

GSE29943 Homo sapiens (human) Non-coding RNA profiling 9 samples Submitted 2011/06/30 Platform GPL11154Platform GPL9115

At a glance

Non-coding RNA profiling · human · 9 samples

What it is: Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism: Homo sapiens (human)
Samples: 9 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Post-transcriptional gene regulation relies on hundreds of RNA binding proteins (RBPs) but the function of most RBPs is unknown. The human RBP HuR/ELAVL1 is a conserved mRNA stability regulator. We used PAR-CLIP, a method based on RNA-protein crosslinking, to identify transcriptome wide ~26,000 HuR binding sites. These sites were on average highly conserved, enriched for HuR binding motifs and mainly located in 3' untranslated regions.

Read the full summary ↓

Surprisingly, many sites were intronic, implicating HuR in splicing. Upon HuR knock down, mRNA levels and protein synthesis of thousands of target genes was down regulated, validating functionality. HuR and miRNA binding sites tended to reside nearby but generally did not overlap. Additionally, HuR knock down triggered strong and specific up regulation of miR-7. In summary, we identified thousands of direct and functional HuR targets, found a human miRNA controlled by HuR, and propose a role for HuR in splicing.

This dataset

Open GSE29943 in finder → Find more human datasets →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE29943_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

Also filed as BioProject PRJNA140779 and SRA study SRP007498. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21723171) ↗

Samples in this study

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

+ 9 more — browse all 9 samples with per-sample file links →

Datasets on a similar topic

GSE324929 RNA-seq analysis of FDX2-inducible knockout (FDX2-iKO) ES2 ovarian carcinoma cells under normoxic and hypoxic conditions 12 samples shares conditions, rna-seq, knock
GSE282012 RNA-seq in keratinocytes knocking down SIRT7 under ionizing radiation conditions 4 samples shares conditions, rna-seq, knock
GSE29778 HuR (ELAVL1) RIP-chip and knockdown exon array 12 samples shares elavl1, knock
GSE330188 Crnic Institute Human Trisome Project - Tofacitinib for Immune Skin Conditions in Down Syndrome: PolyA RNAseq from whole blood 194 samples shares conditions, polya
GSE262597 EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma 56 samples shares conditions, small
GSE262593 EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma (SCLC cell lines) 40 samples shares conditions, small
GSE336731 Transcriptomic profiling of MCF7 ESR1-PARENT and ESR1-Y537S cells cultured under estrogen-depleted or estradiol-supplemented conditions following abemaciclib treatment and CCND1 knockdown 36 samples shares conditions, knock
GSE285142 Effect of knocking down CERS2 or a double knockdown (KD) CERS5/6 in ventricular cardiomyocytes on gene expression under conditions of hypertrophy induced by phorbol 12-myristate 13-acetate (PMA) or controls. 24 samples shares conditions, knock

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.