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Local regulation of gene expression by lncRNA promoters, transcription, and splicing

GSE85798 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 462 samples Submitted 2016/10/28 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 462 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
462 samples: 344 distinct titles, 46 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
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)
Mammalian genomes are pervasively transcribed to produce thousands of spliced long noncoding RNAs (lncRNAs), whose functions remain poorly understood. Because recent evidence has implicated several specific lncRNA loci in the local regulation of gene expression, we sought to determine whether such local regulation is a property of many lncRNA loci.
Read the full summary ↓
We used genetic manipulations to dissect 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis. Surprisingly, however, none of these effects required the specific lncRNA transcripts themselves and instead involved general processes associated with their production, including enhancer-like activity of gene promoters, the process of transcription, and the splicing of the transcript. Interestingly, such effects are not limited to lncRNA loci: we found similar effects on local gene expression at 4 of 6 protein-coding loci. These results demonstrate that ‘crosstalk’ among neighboring genes is a prevalent phenomenon that can involve multiple mechanisms and cis regulatory signals, including a novel role for RNA splice sites. These mechanisms may coordinate the expression of neighboring genes and explain the function and evolution of some genomic loci that produce lncRNAs.
This dataset
Open GSE85798 in finder → Find more mouse RNA-seq 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 GSE85798_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 ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA339437 and SRA study SRP082334. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27783602) ↗
Study design
344 distinct titles, 46 of them repeated
linc1319-PromoterInsertion-150216-G ×4 Gpr19-pAS-151214-G ×3 Snhg3-PromoterDeletion-150126-H ×3 linc1319-Exon4Deletion-150801-D ×3 linc1319-Intron2Deletion-150801-B ×3 linc1319-PromoterInsertion-150216-B ×3 linc1319-pAS-4kb-151214-S1-F ×3 linc1329-pAS-151214-A ×3 +38 more

How we read this: Read from the first 400 of 462 sample titles: 344 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 422 more — browse all 462 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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